The smaller wires can actually be run behind the motherboard itself, freeing room for the larger cables behind the motherboardtray.
I look at air ccooling a case as a "wind tunnel", where you want to have the air flow following a set direction and minimizing the time it spends in the case, as the longer a given quantity of air "sits" in the case, the more heat it absorbs but the less efficient it becomes at absorbing that heat. Just an example with numbers not intended to convey anything other than the hypothetical, if the air is taking 5 sec to travel through your case and the intake air temp is 20C, the first second may heat the air by 10C, the second by 7C, the third by 5C, and so forth. If the airflow is such that it only takes 1 second to travel through the case, you always have air that is absorbing 10C worth of heat. I know that I am not doing a good job of explaining this, but I am feeling a bit brain dead at the moment.
In any air cooled case, my experience tells me that you would want to focus on the following, although every "case" is different and what has worked for me may not work for you.
- Minimize any and all obstructions to airflow (this means everything from cable management to removing unused drive cages, and even cutting out the case's integrated "fan grill" to replace with a wire grill)
- Use higher static pressure and high CFM fans for intake (the higher pressure allows for the air to be better pushed past obstacles while retaining a greater amount of its velocity, and as intakes typically have filters, mesh, drive cages, etc, they need a good amount of pressure or they are not going to be much help)
- Use high CFM low-moderate pressure fans for the exhaust (if you remove the integrated fan grills, you don't need much pressure to force the air out, and exhaust air flow direction typically is not important, so using a fan that will move the most possible air is ideal; this is perhaps the best use of the Scythe Slipstream 1900rpm 110cfm fans IME)
- Design an airflow path, but experiment (heat rises, but in a computer case it goes wherever you tell it to; front/bottom/side intake + top/rear exhaust is a very popular setup, but I have found that front/bottom/rear intake + top exhaust works best for me. Since you have side fans, I would try using all intake with only the side fans as exhaust utilizing some high power fans on the side panel; this may perform similarly to not having a side panel on, or it may work terribly; the only way to know is to try)
- Have internal fans to help the intakes direct their air (mount fans on the drive cage on the inside of the case and aligned with the front intake, as this creates a "push pull" effect prevention stagnation of the intake air and directing it towards the GPU/CPU; if you can fit two fans, even better, but don't have them overpowering your front intake, ideally they should match)
- Upgrade CPU Cooler (The Hyper212 models are popular budget heatsinks, but you can get a lot better for around the same price if you look for sales or buy used; for example, the Deepcool Assassin which uses 8 heatpipes and is a very powerful cooler, has been on sale for $39 which is a 50 percent discount; the slightly older Thermalright heatsinks are also phenomenal deals giving you a top tier cooler for the price of a budget model)
- Use the best Thermal Paste available (Prolimatech PK1 is my all time favorite, but IC Diamond, Gelid HE-Grease, Antec Formula7, and such are all excellent choices; stay away from Arctic Silver 5, as while it was once a great paste, it'swwell past it's prime and will not offer much if any improvement, and the newer pastes don't require a ridiculous month long cure time)
- Use Active or Passive cooling for any heat generating items (get some VRM, MOSFET, and PLL heatsinks and use them on anything that produces heat; a relatively small and quiet 80x15mm fan pushing just 15-20CFM, situated over the motherboard VRM heatsinks, can drop temps in this area by 10-25C, providing cooling to the most important part of the motherboard and I have seen it make stable otherwise impossible OC's)
- Replace the TIM on the motherboard heatsinks (VRM/MOSFET and NB/SB heatsinks can hugely benefit from a simple "remove, clean, apply, replace" as the factory stuff is usually too great in quantity and too low in quality; Intel boards benefit from the VRM sinks, while AMD benefit from all of them, though on any board I'd switch the paste for all of them anyway; use something like PK1 which is not electrically conductive)
Doing just the above, I have seen temps drop by 20-50 percent in various systems, and in every case the computer was able to overclock quite a bit higher, yet still run cooler than before.
Air cooling is liked by many because of the low risk/high reward, the low expense, and the seemingly ease of use. However, it is far more complex than many would think, and to do it right requires the willingness to experiment, and a lot of patience! Doyll is one of the people who I would consider to have "mastered" the art of air cooling, or at least is well on his way. I would trust his advice, but don't be afraid to try something new, different, and maybe even seemingly counterintuitive, because it may just make a difference for the better!