Might I see what it looks like?
I don't build fuel stations solely because I either 1) try to maintain enough fuel to get around Kerbin/Mun/Minmus/re-entry and 2) I use fuel-efficient ion engines and inductive thrusters for longer journeys.
I would start by getting the main core of the station into a 120km orbit. Attachs docking nodes where needed. Then i'd fly very large individual tanks (probably like 4, 2 on each side of the station) up with RCS to a 100km orbit. Alter it until you rendezvous and then dock the tank. Ta da, fuel station.
If you are trying to get this one big, heavy structure into orbit as one piece, that's most likely the problem.