the more aero wheel should be on the front anyways since the seat tube cuts most of the air that would hit the rear whereas the front has nothing to stop it.

The best thing to do would be have a rim in back that's deeper than the front. It's pretty common, for example, to see a bike with a Zipp 404 on the front and an 808 on the rear. There are a few reasons for this:
A more shallow front wheel is easier to control in strong crosswinds. That's why you don't see disc wheels on the front, except on some track bikes.
A lot of or all of the rear wheel is in the turbulent shadow of the frame and rider. A deeper rim is more likely to encounter less turbulent air flow or better control/manage turbulent air flow.
A deeper rim on the rear doesn't complicate bike handling/steering as much a deeper rim on the front.

With regard to aero wheels, keep in mind that the best aero wheels only add about 0.4 mph at 25 mph. Don't expect aero wheels to perform performance miracles. With that said, aero wheels can make a significant benefit on long and/or fast descents, and aero wheels are now available at some pretty damned reasonable prices.