Method for aligning docking ports across modules

[Duke23]

I haven't seen much info on this (apologies if I just haven't looked hard enough) but I know you guys are doing it, so here goes. I've been messing with these tanker stations in ~125-150km Kerbin orbit for my outgoing gas guzzlers and to experiment with docking configurations for orbital ship building other than in a straight line. I want to have my pieces arranged rotationally correct basically so that if I build something large I can fire the engines off in pairs and not have the ship cutting cartwheels through space like my Minmus mission (single docking ports) where the outside engines were .1 degree off from each other. My first dual port design worked pretty well, which was to just pick lines on the tanks and reuse the same core with docking ports already placed.

Problem is what if I want to put something different onto the same ports? I am scared to just guess how far apart to put them and hope it works. So I tried this method:

It's just a bi-stack adapter with a battery as a spacer to prevent clipping of the docking ports out the backside of the adapter. It's gotta look nice too right? The battery packs aren't heavy and I certainly don't need that much electricity but the problem is it doesn't seem to be very stable. It already flexes just when I rotate the station, I'd hate to throttle up the outside engines. And I can't exactly hang that huge assembly off just any payload coming into orbit, it'd be silly. That and it leaves my connected modules miles apart, which in this one case is perfectly fine.

Basically I'm asking is there a reliable way to place dual or more docking ports that I can make it standardized for use with all my building needs and won't fall apart or add too much extra crap to my ship? How do YOU make sure your orbitally constructed vessels aren't going to shake apart or thrust different directions? Maybe I'm missing something here.

Edited December 31, 2013 by Duke23

[zxczxczbfg]

I make sure they don't thrust in different directions by using MechJeb's docking guidance and enabling "Force Roll" on both ships.

[Duke23]

Ah, I see. I tried MechJeb once and it's pretty cool but I prefer to control everything myself for something "serious". The only mod I'm using right now is a docking alignment indicator.