Problem with docking and stages

[A.H]

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.

[Not Sure]

Staging gets risky is ksp, there are quite a few glitches and such that will ruin your day so if you’re in interplanetary space or in orbit, it is sometimes safer just to right click on objects and activate them manually. 

However you can re arrange your stages in the flight scene by dragging them up and down just as you would in the VAB. I’d advise doing this after docking or undocking and firing the engines manually as sometimes it will skip a stage.

Edited December 1, 2017 by Not Sure

[Corona688]

"What should happen to stages of two docked craft" is a pretty tough question.  Every "good" way I can think of ends up being good for a few of my designs and terrible for the rest.  Just rehecking everything seems to be the way to go.