Hi Chad,
If you bought two copies of After Effects, that means you have two distinct serial numbers. You can install After Effects on as many machines as you like - its the amount of times you can use a given serial number and activate against a product that will restrict you from using on more than two machines.
If you go to http://www.adobe.com/downloads/?ogn=EN_US-gntray_dl_trialdownloads, you'll find that you can download (and consequentially) install After Effects on as many machines as you like. Again, if and when you serialize and activate successfully the product will determine how long you can use the product (30 day trial vs. activate with a valid serial number). Since you bought two copies, you have two SNs, and you can use those two SNs on a total of four machines. The EULA specifies this.
The EULA can be found at http://www.adobe.com/products/eulas/.
Best,
-Marcel