This is definitely possible with After Effects CS5 and later, but I don't believe that it's possible with After Effects CS3.
See this post for more information:
is an Administrative Install Point possible with the CS4 suite?, or will I be facing the same issue?
If you follow the link that I gave, you'll find the blog and other resources from the team at Adobe responsible for deployment and isntallation. They are much more able to answer these questions than those of us here on the After Effects forum who mostly know After Effects itself, not the deployment system surround Creative Suite software.