Ok if you don't need an unlock then you can just hit upgrade. You won't lose your apps/music if you select "transfer purchase" by right-clicking your device in iTunes. Then syncing. You'll need to restore from back up after upgrading to 4.1 to keep anything else like photos and contacts. It's not recommended to restore from back up as it could carry over or create problems from previous jb, so you might wanna set up as new instead and back photos and stuff up to your comp. You could try restoring from back up if you've got a lot that you can't back up manually, but that's up to you.
I see... so basically to recap the steps for those on 3.1.3 spirit JB... (also for the convenience of TS)
1) Backup all apps and stuffs on iTunes
2) Just go straight to upgrade to 4.1
3) JB using GP
4) Restore apps (might complicate matters)
5) Upgrading the iTunes (I guess this is necessary although not mentioned before)