The business rules don't change - you are allowed to install and run one copy of an Adobe product on two machines. However, there is a finite amount of times where you can deactivate your license. This is done to discourage "floating" the license between your machines.
However, in your case, since you are buying two copies of After Effects, you can essentially install and run on four machines (two per unique serial number). So in your case you are fine and complying with the EULA set forth by Adobe.
Thanks for your concern regarding license compliancy!