To be safe, you always shut do a full restore (I even like to DFU mode, but probably not necessary) before jailbreaking. Just ensures you have a "clean" system.
You don't want to screw things up and have to restore only to find you can't restore to 6.1, but 6.1.1 or an update that patched the jailbreak.
Is it okay to restore from backup or do you go by the theory to set up as new?