Having trouble fying docked ships

[OUScooby]

So I designed a two stage lander that I was hoping would take me out as far as Jool and back. I launched both the orbiter and the lander into orbit around Kerbin and docked them nose to nose, so that the lander is connected to the top of the orbiter bu facing in the opposite direction. The first problem I'm having is a minor one and that is the way the two ships engines are combined in the stages when I dock the ships together. It seems to automatically combine the both final stages together, both 2nd stages together and so on. I've got an OK work around for this but I was wondering if there was a way to prevent it.

The next problem is really the one I need help with. As I said I've got the two ships docked nose to nose, and I fire up the rockets on the orbiter ship and the coupler fails and the orbiter drives itself into the lander, followed by and explosion and 5 dead Kerbanauts. What am I missing why wont my ships stay together and fly as one?

[Psycho0124]

Sometimes you're going to be forced to rearrange your stages when you dock two ships. It's a pain but I don't know of any other way to sort things out.

As for both engines firing, right-click the opposing engine and click 'deactive engine'.

[Kialar]

OUScooby: I guess we have a similar issue here. Do you agree?

http://forum.kerbalspaceprogram.com/showthread.php/31197-Rocket-parts-slide-into-each-other

[OUScooby]

Sometimes you're going to be forced to rearrange your stages when you dock two ships. It's a pain but I don't know of any other way to sort things out.

As for both engines firing, right-click the opposing engine and click 'deactive engine'.

This actually seems to have solved the problem. What was happening was that even though I moved the engines from the lander ship out of the current stage they still fired when I fired up the engines of the orbiter. I'm not sure why this would happen even after I move them to a different stage (and I still don't see why I can't put them in the order I'd like), but I guess they massive explosion and needless loss of Kerbal life was due to the two ship trying to accelerate into one another. De-activating the lander's engines solved this. Tomorrow I'm going to take her out to Jool and see what happens. I've got a Kerbanaut stranded on Lyathe I want to rescue, and on the way back I'm hoping to pick up another Kerbal waiting patiently on Dres. Fuel (and orbits) permitting I might also try to pick up another stranded traveler who's orbiting the sun after running out of fuel on the way back from Duna. That would take care of all my stranded Kerbanauts and clear my conscience for the start of new adventures in v.20.

Here is the pic to my 2 stage craft, I welcome opinions feedback and criticism:

[PaleoGamer]

If that doesn't completely solve your problem you might look at Quantum Struts. That mod adds "struts" between the two docked vessels making them more stable during maneuvering.