I have played KSP for quite a while now (and love it), but only recently have started using docking ports.
for a minmus mission I decided to go with a lander vessel on top of a large carrier vessel joined by two docking ports.
I tested it in orbit over kerbin, and it I could undock and dock it with no problems, except that after docking again the stages of the lander vessel are merged with the stages of the carrier vessel.
Is there a way to prevent this from happening? Or should I build the craft differently (Now I have built both in one go, no subassemblies)?
What I would like is the staging sequences of the two vessels to be kept separate. I don't even need to see the stages of vessel2 when controlling vessel1 (and vice versa).
Hope someone can advice.