When you talk about the CUP cooler, most of time it will block the RAM if you install the aftermarket cooler. And you can install the RAM into the 2nd/4th slot to avoid the cooler. Which cooler will you install in the MB?
If you use two GPU yes the heat will increase inside the case, but if your case has good airflow then there is no problem.
Obviously you understand that you need a CPU cooler of some sort, but depending on whether you plan on overclocking the CPU or not will depend on whether you stick with the stock cooler or whther you buy an aftermarket one.
Generally GPU's come with coolers attached, and these coolers keep the GPU itslef cool and do not really contribute to the temperature control of any other component. But it doesnt matter whther you have 1, 2, 3 or even 4 GPU's, the amount you have will not change the temperature of the CPU by very much. the only way you would benefit from a better CPU cooler with multiple GPU's is if the GPU you buy does not have a very effective cooling solution on it. If the card expells most of the air into the rest of the case then it may be adviseable to buy a better CPU cooler than the stock one, but most modern GPU coolers are designed to expell the majority of the heat from the exaust grills at the rear of the card (The bit that you can see from outside the case. You may see a couple of degrees difference by adding an aftermarket CPU cooler, but providing you dont plan on overclocking either the CPU or GPU's, you will be fine.
what cin19 said was correct, make sure you measure up how much room you have between the current CPU cooler and the RAM, to make sure that if you do buy an aftermarket CPU cooler it will not obstruct any of your DIMM slots.
If you need any more help with the build, please do not hesitate to post further questions. =)#