The fun thing with PCs is that you can do whatever you want to do to them. if you are looking for performance/best cooling you should stick with how hear naturally moves, upwards. most people use the front and bottom fan slots as intakes, and the rear and top as exhaust, however the rear fan can also be used as an intake, to bring more cold air into the system, while still leaving the top as exhaust with the H100i.
personally i would use the H100i as a top exhaust, here are some reasons as to why:
- the top of cases are usually not filtered, so if used as an intake they will suck dust into the system, and with a side windowed PC it is much more noticeable, because most of the time people look at their windowed PCs a lot.
- The H100i has 2 SP120l fans in it, not bad looking fans, however if placed in the intake position all you will see is the rear of the fan that's not that great of thing to look at. however if placed in the exhaust position you can see the normal side of the fan, a much more pleasant experience, and if you want to upgrade you can do the whole LED or color matched thing.
- In the exhaust setup you will be pulling hot air form your CPU out of your case, not pulling it into your case making the system hotter as a whole.
- Dust..... Whatever you do make sure that you are keeping the CFM of your intake to exhaust the same or positive. lets do a hypothetical, you have 2 120s in the front, 2 in the top, and 1 in the rear, all are the same RPM/CFM. you'll need to keep 3 of the 5 fans at intake in order to keep the airflow even, and have 1 extra fan pushing air out of the small cracks in the case.
https://www.youtube.com/watch?v=g8EN3K-eaVA
Here's a short video to help, i'm not the best with words ^^
So if you filter that intakes, as well have more intakes than exhausts you should be fine, and you'll just have to figure out what you want to do for the best aesthetics, if you even care. also for a side note, i don't know exactly what fans you'll be using, but you will probably want to get silent optimized fans for the front and rear and silent Static Pressure fans for the H100i. the R4 is a silence optimized case and if you throw some cheap fans that sit at 100% all the time in it, it'll be a shame, however this is just my personal opinion, yours my differ or you may not have the budget to get fancy fans that fit your build perfectly.
Also if i said something wrong in this i'm sure that someone with a bit more experience will catch the error and correct it.