That is one of the reasons I use a homescreen replacement. Since it's an app, it gets backed up as well with Titanium Backup and then is easy to restore. It takes me WAY too long to setup all of my screens. I am currently using Go Launcher EX (free in the market), so it's just a matter of backing up using TB, modding my phone, then re-downloading TB and restoring my apps, and my screen is back exactly as before. Used to have trouble restoring widgets, but that seems to work now.
So Go Launcher Ex would be my homescreen replacement that can be backed up with TB as an app?
Or, you could take snapshots of your homescreens and re-set everything up. Uggh.