Here's my build: http://pcpartpicker.com/p/4RFRgs
I'm gonna make it soon, the case have a filter just under the PSU Area.
What do you mean by flipping it?
If it has a vent on the bottom of the case for the psu, then aim the psu fan at the vent... That's so it can get fresh and cool air.
Unless you have it on carpet, flipping it so that the fan is face down gives your PSU fresh air from outside which is always beneficial
If it IS going to be on carpet, put something hard and flat under it like a piece of plywood or sheet metal
Nah, it's on my desk. But does the PSU really needs a lot of air?
Just do it. It's always better to isolate the PSU from the rest of the components. Having it pull in air through the bottom filter will allow it to stay cooler than if it were pulling in the hot ambient air inside the case. Cases these days are all designed to have the PSU oriented this way.
It depends on (a) if you have a filter under the PSU (b) if you're in the positive pressure or negative pressure camps (c) other fans on the case and whether they blow in or out.