First off, I'm to the point where I have to connect the power from the front of the case to the motherboard, It says there is a positive and a negative, but the power cord coming from the case doesn't explicitly state which is positive and which is negative. There is an arrow on one side, would this be the positive?
I know this is the part where you really dont want to mess up.
Also, I bought an SSD, a HDD and a disc drive, but it only came with 2 SATA6 cables, could I use the disc drive to install the OS to the SSD and then unplug the disc drive to hook up my HDD?
I can't be sure about the first question but you can definitely take out the SATA cable after installing your OS then put it in your HDD.
Okay, I have another question to. I have a cable coming from the front panel that says 1394, it looks like it will fit in JCOM1 Serial Port connector, would it be okay to plug that in too?
No, 1394 is the internal header for Firewire (800 i believe)
The COM port usually goes unused in 99% of builds.
By "Power from the front of the case to the motherboard" do you mean the power LED and power button???
if it's the switch: it doesn't matter, it will work either way
if it's the led: one way the led will work, the other it won't, it won't damage anything you just have to flip it if it doesn't lite up
The cord from the power button, power led, reset switch, HDD LED, and Power LED.
The motherboard lists them as positives and negatives, but the case doesn't say which connector is positive or negative.
Also, do you know where the 1394 cable would plug in? USB maybe?
Q1. For the front panel connectors it wont matter what way you plug in the power and reset switch. As for the LED lights if you plug them in and the lights don't come on just flip the connector around.
Q2. you can do exactly what you said, connect up the SSD and CD-ROM and when done just switch the CD-ROM to the second drive.
Q3. 1394 is for fire wire and need to be connected to a fire wire connector on the main board. using a serial port may damage something
No the 1394 only plugs into the 1394 connector.
The power button and reset button dont have a positive or negative so it doesn't matter.
The LEDs will either work or not, so if they dont, just flip the connector around