You also need to be aware that commercial jump engines can not take a military engine ship through jump points.
As for what to put on to pad out the spaces, I like to use my jump tenders in one of two ways. The first is equip them with the biggest passive sensors I can. The second is to equip them to support the rest of the fleet with extra mainenance, fuel, or missiles. With the current game setup I would also add some emergency cryogenics and extra crew quarters to handle either prisoners or if one of your ships is destroyed, you have a place for the crew to go to.
Brian