The good thing is, that you have some versatility: most of these coolers come with hardware that allows you to mount the fans hanging outside of the heatsink in either side – leaving the option open for even a 3rd fan being added.
The P9X79 and other s2011 motherboards with dimm-slots on either side of the CPU socket cannot take advantage of this, unless you will be using less than 4 dimms. Most AM3+ and LGA1155 boards have their 4 dimm slots arranged on the right of the CPU socket (opposing the I/O ports). Many of them though also have a smaller area around the socket and/or might have the dimm slots closer to the socket as the relative
CPUs are smaller than the s2011 package. In that case, the heatsink might not require the addition of a fan to obstruct the usage of the slot being closer to the socket when a dimm with a large heat spreader is required to occupy it.
When we add the fans on the cooler, we have potential issues with not one, but three of the dimm slots on the side where the secondary fan is mounted on. In the photo below you can see that full size dimms – bigger than the low profile PCB Samsung sticks that I am using, would barely clear a couple of millimeters. Low profile heatspreaders on full size dimms are fine, as the mounting springs allow some play for the fan to be re-positioned from its self-sentering point you see below. It will still be resting on the dimms , but at least allowing the slots to be occupied without issues).
A possible issue with mounting the secondary, or a third, fan closer to the rear exhaust case fan that most enclosures provide, is the two fans being too close to each other and the air flow resonating between them increasing noise and even hurting overall cooling performance, in which case the solution would be removing one of the two fans.
It is also possible to mount the coolers with the fans facing upwards (or downwards), but then you will probably have issues with obstructing the first couple PCIe slots on the board, and having the PCB board of your GPU obstructing airflow to your CPU cooler (and radiating heat right next to it).
I hope the above gave you a proper idea of the issues that might come up, so that you won’t run into surprises when you will try to put together your hand picked PC build. Remember that it makes little sense down-grading your CPU cooler, or opting for a sub-par AIO watercooler just to solve this issue. If possible, pick the right sticks to begin with, or plan ahead to experiment when mounting the fans.