Standalone Flash Builder 4.5 is still Eclipse, just that all the Adobe plugins are already in place. So installing additional plugins is same as with standalone Eclipse.
You can:
- go to Help / Eclipse Marketplace and search for Tomcat: I just found Mongrel plugin stating following "plugin for running tomcat (incl. ability to debugging tomcat apps or tomcat itself) from within eclipse
- go to Help / Install New Software, select appropriate site and install Tomcat plugin (you'd have to search for the site, eclipse install site might be a good candidate)
On my Mac both sit in Help menu, on Windows it should be the same.
What I've just noticed inside Preferences - if you go to Server / Runtime Environments you should see "Download additional server adapters" Link. I have just clicked on that and see a lot of adapters, unfortunately no Tomcat.