One thing about RockSim - you can place any length of engine into the rocket, in any tube that you designate as a motor mount, regardless of whether or not your design even has the physical room for it. You can even load engines whose diameters exceed the diameter of the rocket!

For a realistic sim, you have to be careful to use an engine that will actually fit, and place it where it would actually go in the real rocket, so that its forward end stops at the engine block, or at least doesn't extend into a solid bulkhead or transition (RockSim won't do this automatically for you). For reloadable motors, you have to know the width of the thrust ring on the aft end of the case, and then adjust the overhang number to match this width when you load the motor.
I have had fun doing virtual launches of rockets with motors that are so long, they need to extend several inches out the back of the rocket. This doesn't mess up the stability margin as much as you would think! In fact, quite often the rocket is still quite stable without needing to add a mass object in the nose.
MarkII