Please go watch some basic hardware build logs for the absolute basics of computer parts guides. I highly recommend Singularity Computers on youtube, he does a lot in terms of custom rigs and really long and thorough build logs for them, but he also does some pretty basic ones. Linus Tech Tips on youtube is another good place to check, as is the Razethew0rld channel on youtube. Especially for the basics of overclocking. In terms of a first time build, you may want to stick with intel if you don't plan on overclocking, or go with AMD if you do. AMD is more forgiving, but Intel is usually more powerful out of the box. In terms of parts going where, they have slots and cards that are designed specifically to go only one direction, if it doesn't look like it won't fit, then it doesnt go there. First of all, make sure you have the proper number of standoffs in the motherboard tray of the case, if you don't see a threaded hole through the motherboard's mounting points when you place your motherboard in, then install some of the extra ones that came with the case. If you happen to have too many, and you are bumping the motherboard against them, make sure you remove the offending part before installing the motherboard. Check your aftermarket cooler before installation to make sure there are no additional instructions for installing a backplate, if there are, follow these before installing the motherboard. It may be easier to install the CPU and heatsink outside of the case. The CPU will say which socket it is designed to go into, and if the motherboard says it is designed for that socket, then it is going to fit, just lift the lever for the socket and match the little triangle in the corner, drop the CPU into place and lower the lever. to install the thermal interface material properly, I would recommend checking with Arctic Silver's website, as they have thorough guides for things like the proper application technique for each processor type and for things like tinting the heat spreader and cooler block, and how to deal with heat pipes. After you have that installed, you can either move onto the RAM and get that done before installing the motherboard, or you can do that after. With the RAM, you open the levers on the RAM slots (There are usually four right next to each other, they have like, 240 copper contact pins in each of them, so they are pretty noticeable) then position the RAM module so that the notch lines up with the plastic protrusion within the slot, then insert and push straight down, applying even pressure until the clips click back into place. After installing the RAM, you should go ahead and install the motherboard. Make sure the serial connector panel (sometimes referred to as the backplate or the I/O shield) is installed by checking the orientation of the holes against the connectors on the back of the motherboard, then pushing it through the hole on the back of the case. Make sure that you are pushing it from the inside of the case so that the raised spring-ey prongs are pressing against the inside of the case, as this keeps it pressed firmly against the motherboard to prevent it fron shifting or rattling. Make sure that you push it in until it makes a satisfactory clicking noise. After that, line up the motherboard with the backplate and gently push the connectors trhough their appropriate holes and line up the mounting points with the standoffs and screw them in. Try to screw them in until they are finger-tight, in a star pattern so that you don't put too much stress on the board. Then go through and tighten them until they are snug, but not overly tight. PCI-e is pretty easy, if it has a retention clip, push it down so that is is out of the way, push the card in until it clicks, screw it into the case. PCI-e x1 and PCI are similar in that they only fit into their designated slots, just make sure to check that all of the explansion cards that you want to run are supported by the connections on your motherboard. After that you connect up your power supply cables to what they fit on, it is all very intuitive as they are keyed so that they won't fit unless they are meant to go there, so don't apply excessive force to any of them, if they don't appear to go there, they probably aren't meant to. I would highly recommend watching some videos to get more in-depth knowledge of connectors within your computer, as it does tend to make differentiating between an EPS 8-pin CPU power cable and a PCI-e 8-pin GPU power connector a bit easier.
Overclocking is a very long story, but usually CPU-based overclocks are done trhough manipulation of the bus clock and the base multiplier settings within the BIOS of the motherboard. If you are looking to do some overclocking then you want to get a Motherboard that not only clearly supports it, but that also has the appropriate numger of power-phases to actually accomodate it. A power phase is the power manipulation and delivery mechanism that the motherboard employs to ensure that the voltage and amperage of the power that the power supply is feeding it is exactly what the individual components need to function. This becomes especially important as you overclock tot he point that you begin needing to increase the core voltage of the processor or the RAM controller, and you start running past the manufacturers recommended stock range. Because it is usually the voltage increase that will kill your components before the heat does. Now then, GPU overclocking is often done on the software side of things, since it has to function through a driver in the first place, so it requires almost no additional effort for it to adjust things like the core clock rate and the memory clock rates of the component trhough the software interface with it. Most brands will have their own overclocking tool, but if all else fails, MSI's afterburner tool will usually do the job, and it has a handy testing tool based on the furry taurus test from Kombustor, which is good for a thorough burn-in as you can see what happens to your temps and framerates live when you adjust settings. This is especially nice as it doesn't bother throttling your GPU as the temps climb, so you can see what you should expect to hit in games, which also don't throttle your GPU.
No, often it is not worth overclocking on your first build, because it is horrible to get it up to a moderate overclock only to have something go wrong and fry your build. This is why AMD is more convenient, as their parts are more forgiving than Intel's, if not simply due to the much larger architecture, which makes increases in voltages not cause a huge amount of interference problems.
Cable management is a vital part of computer builds, but it honestly isn't THAT important unless you: a.) have a windowed side panel or b.)know what you are doing. If you have neither, your greatest concern is just to make sure that your cables stay out of the fans and off of most metallic objects that are attached to your motherboard. These include heat sinks, heat spreaders (the heat sink-like thing on RAM) and other various accessories and components that may not appreciate having a cable wedged against them. If your case has area between its motherboard tray and the back panel of the case (usually indicated by having holes cut out of the motherboard tray at strategic points near the edges of where the motherboard will go. Also sometimes these holes have rubber or silicon grommets to make them look better) then you should make some attempt to run the cables through these and behind the motherboard, only dragging them back through another hole when you need to plug them in, then you try to draw them through the closest hole to what you are trying to plug in. Some motherboard trays have really tall standoffs because they intend for you to run the auxilary motherboard power cable behind the motherboard (That EPS power connector I was talking about.)
Good airflow is entirely decided by the amount of venting your case has and by the position and number of fans that you have in it. Do not necessarily concern yourself with having a huge number of fans, simply that the number of fans drawing air into your case through some sort of filering mechanism (look up fan covers, filters and grilles) are greater than the number drawing air out of your case. By doing this, you get dust caught on the things you can more easily clean (your filters) and it blows air out of all the other holes to keep dust out of them.
And a good basic rig for starting out (by totally beasting everything):
http://pcpartpicker.com/p/Hbok
And For slightly less expensive and a little easier to install:
http://pcpartpicker.com/p/Hbrt