Eric, I also recently received some enclosures… this is my two cents,
YMMV, etc:
If the fan is installed such that it blows in onto the USRP, it will
receive the direct benefit of the airflow. However, the fan makes a lot
of noise in this configuration because the blades are right next to the
perforated enclosure wall.
Turning the fan around so that it exhausts air from the enclosure makes
it quieter, but the airflow pattern has major components that enter the
enclosure on the fan side and get blown right back out, providing much
less cooling airflow over the USRP itself.
The solution I decided on was to mount the fan in the exhaust mode and
tape over the holes on the fan side of the enclosure (other than the
holes covered by the fan, of course!) This arrangement produces maximum
laminar airflow over the entire USRP assembly and minimizes noise. I
find that clear packing tape works very well; it’s just the right
height, and it makes for a very clean installation if you put it on the
inside of the case. If you really want to be a perfectionist, don’t
forget the holes between the fan and the front of the enclosure. 
The only downside to taping the holes is that in case of fan failure,
you have significantly restricted the opportunity for natural convection
or external forced air entry. I assumed that, if the fan is a design
necessity due to heat load, losing the fan would be a problem regardless
of the number of air holes and would need to be addressed anyway.
Good luck,
Mike