Normally, a backup restore of your iPhone 5s should have affected the restore process on your jailbroken iPhone 6s. The cause of the iPhone 6s hanging on Apple logo is not due to the restoration operation, rather something else with your iPhone 6s it self, or with iTunes or the 3rd party software you use (in case you are using a 3rd party software to do the restore).
I have always jailbroken my new iPhones before doing a restore because I need to know how much of space the jailbreak is taking on my new device, if it takes more than 600mb, then I would restore it and jailbreak it again. Only after that I would restore my backup from the old generation iPhone to the new generation iPhone.
Now that your iPhone is stuck on Apple logo, you can try to put the iPhone in safe mode since it's jailbroken by pressing the up volume button as soon as you restart the iPhone and see the Apple logo. Keep the up volume key pushed until you see the lock screen. It could take 1mn to 3mn maximum for the device to enter safe mode. Try it several time if it fails the first time. If that fails, you will have no other option than putting the iPhone in DFU more and perform a factory restore, which of course will force you to iOS 9.2 you will then have to wait for a jailbreak to be available for that iOS version.