Controlling two vessels at once

[Rivelin]

Hi. I've only been playing KSP for a few days so I hope I'm not missing something really obvious here (I've done plenty of searching for answers though to no avail)!

I've built a plane that can carry a rocket and I've been trying to figure out how to do air-launches (like how Pegasus rockets are launched IRL). The part that causes the problem is having two vehicles to control after the rocket is separated from the plane. I've been learning how to use Mechjeb to try to achieve this. I was hoping to first control the rocket after separation, use Mechjeb ascent guidance to start it climbing towards orbit then quickly switch back to the plane and land it manually. However whenever I try to do this after switching back to the plane, the rocket just disappears, I go to map view and can't see it at all. My plane has a Cockpit and the rocket has a Remote Guidance System. I guess what is happening is that when I switch from the rocket back to the plane it becomes uncontrolled and just falls back to the ground? Is there any way to do what I'm trying to do or is having two vessels under power and under control at the same time just not possible?

On a different note, I had been taking a spaceplane into orbit and struggled to figure out what it'd always reentered engines first. I finally realised that I was using a Command Pod rather than a Cockpit, changing to a Cockpit stops the problem. It seems like the way the Command Pod is designed always makes it want to re-enter blunt side first, even to the extent of rotating a large aircraft to come down backwards! Coming through the upper atmosphere rear end first, entering a flat spin and trying to desparately recover in the last 5000 metres isn't a very elegant or reliable mode of flight for a reusable spaceplane