Your best bet is to continue to use iTunes to back up your jail broken iPad. iFunbox is good to get photos and such from your iPad, but it's a more onsie/twosie thing. It's not designed to do a whole system backup as iTunes does.
In other words, I don't know how to do it because I don't think it can be done - at least not a full backup as done by iTunes.
Marilyn
P.S. And, since you talk about a jail broken iPad, I've taken the liberty of moving your post over to the Hacking section. Thanks for your understanding.