how did you jailbreak your iPhone? did you factory reset the iPhone and then jailbreak? or you jailbreak it without factory reseting the iOS? depending on how you jailbreaked your iPhone usually iTunes will still recognize your iOS even after you jailbreak it unless you factory restore it and then jailbreak it right away.
You can chose to set it as a new phone and then start from there, iTunes will not mess up with your iPhone if you set as a new phone. And in case you are already having applications in your iPhone and want to since them with your iTunes you should go to file and transfer purchase from your iPhone to your iTunes and your will not lose you apps from your iPhone. As for the musics present in your iPhone, you can resync them again into your iPhone since you already have them in your iTunes.
