I have used both, plus Pinnacle. My experience with Jeppesen has not be stellar. They will not react to changes as well as Universal. If there is a last minute change or a problem, Universal will pick up the phone and call directly. Jeppesen picks up a computer keyboard and sends an e-mail. It really depends on how stabilized your trips are. If they are set in stone, Jeppesen is fine. If there are last minute changes to destinations and the like, I think you will find Universal more to your liking. Lets face it, while the boss may like to keep costs down, he is more interested in results. If he can't do what he wants/needs to do, you're the guy who gets it.
One thing I do like about Jeppesen is that if you have access to Jetplan.com, you can do your own flight planning and just give Jeppesen the flight plan number. That way you have a little more control over your routing.