It depends on the motherboard. If the controller is already wired to control a cooling fan, like the FlashForge Creator Pro, then it’s an easy matter to hook it up. That’s idea, because then it’s under software control so you can have your slicer control the fan, so it can be on for PLA prints and off for ABS prints. There’s no particular risk to doing this. Watch the video that 3DAmigos printed, and if that looks scary to you, don’t do it. To me, it looked like 15 minutes work - the hardest part is running the wiring up the guide tube!
For other controllers, such as the Makerbot Replicator, the controller board could drive a fan, but you have to solder a chip to the board, so that’s more work (and risk of damaging the controller). Some controllers don’t have any capability to control a fan, in which case your only option is to power it externally.