How does one upgrade a jailbroken iOS device?
You will require iTunes. Connect the device, then right click on it in the iTunes side bar. Select "Back Up." Allow it to runs its course. Close iTunes. 

Then put the device into DFU mode:

1) Power off the device.
2) Disconnect it.
3) Hold the power button for 2 secs.
4) Without letting go of the power button, press and hold the home button for 10 secs.
5) Let go of the power button but not the home button for another 10 secs.   

Reconnect the device and launch iTunes. It will detect your iPad and inform you it is in recovery mode. From there, it will check for the newest available update (5.1), download it and install it. When that completes, simply restore your device from the backup you made earlier.