Bess has all the blueprints in her inventory. Take them all out. Click on the one for the Academy. If you can't build it (due to lack of materials) it'll tell you in the top left-hand corner of the screen.
If you can build it it'll show a message that it's been loaded into the construction set. Hit your 'build' key (usually C) and wait a few seconds for the mock-up to appear in front of you (I assume it appears like the toilet did). Then place it where you want it to go.
I haven't built one yet, not enough materials or builders available. I had an issue with the workbench so had to re-start the mod as I couldn't then build anything new. It was no fault of the mod, but my own :unsure:
Edit:
This sounds awsome, what RTS mod, I am intreagued. Someone please explain/link?
http://www.fallout3nexus.com/downloads/file.php?id=7070