For the 'orbital decay' due to atmosphere (2nd problem), you can just apply some drag if the object is in the atmosphere.

Calculate the resistance force and apply it in the direction opposite to the velocity vector (as in slow down using that force)

IIRC

drag = objectCrossSectionalArea * objectSpeed^2 * airDensity * someConstant

where airDensity is a function of distance from planet center (or surface, doesnt really matter), see wiki article (seems complicated, so maybe you can just try a few simple functions like constant, linear, exponential etc. and see what works best).

You might want to not apply atmospheric effects above a certain altitude (define some cut-off point), so anything above that altitude wont be slowed down due to atmospheric drag.

A simple model would be constant air density + cut-off at some height (like in that angry birds pic, you could draw similar 'atmosphere circle' with constant air density inside and no air outside), which might be how angry birds does it.