I think the only changes you'll have to make are the path to the file server and the ssl cert for the reports server.
The file server change is done by some sql scripts, look in the install guide for 'use the database to change file servers'
the reports change should be done w/ 'blrptadmin' - something like set reports host
there's a gen command to re-generate the ssl cert
There is a GUI that is installed with the CM (under Bladelogic/ utilities) on Windows called:
Application Server Configuration Wizard
This GUI has a tab for File Server and Database information. I'm wondering if I change that information in the gui, will I need to run the scripts manually?
Yes, the db scripts update all the existing items in the database w/ the new file server path (path includes the server name).
That wizard is really only used for the initial configuration - to change settings on the appserver after the initial install you'd want to use OM\bin\blasadmin to update database settings, etc, except of course for the file server setting. For that you must use the db scripts.