Fuel transfer should work as the Jrs are fuel cross feed capable. I haven't tried it yet, though. I've launched full fuel tanks. For the worst case, my tanks have a docking port directly attached to them so I should be good. Edit (just remembered): I've transferred monoprop to different station segments from my fuel tanks. So it does work. I've used the subassembly loader but could've done without it. The trick is to load the fuel dock frame (the part attached to the station), add the tanks with all parts (you want to get the correct height) and the build the lock part to match it. I couldn't attach the lock part to the tanks in the VAB so I've unattached the whole tank/frame part (red translucent in editor) and eyeballed the correct sizes. To make sure it works you could build test rovers and try the docking on the launch pad I guess. I did it the Kerbal way: eyeballing and trying it in space first