The ATX case with a top-mounted PSU was designed in anticipation of that PSU being a part of its cooling; in a case with a bottom-mounted PSU, make sure you have at least one rear or top fan to exhaust heat.
A bottom-mounted PSU with a 140mm fan can usually be turned either way. Fan-down, it draws cool air from beneath the case. Fan-up (or if it has an end-mounted 80mm fan), although it can help move air through the case it may not contribute as much to cooling because it is fighting physics (warm air rises). A front or side-mounted intake would probably be good to have if the PSU fan is facing up or is an end-mounted 80mm.
Personally, I prefer the bottom-mounted designs because they also tend to be more stable, and cable management is typically easier.