Are you creating the grip models from scratch or are you buying the models and just trying to line them up?
Honestly I'm not sure I would use double sided machining for gun grips since they are different from left to right. Anyway that's you call.
As to what side you are working on, Vectric did put up a big "dummy your working on the back side" sign. Besides the material with an arrow on top or bottom icon at the top menu bar there's a big yellow border around the work area of the back/bottom side.
If you are using two models for the left/right (front/back) grip and are having trouble lining them up. Take one of the models and create a bounding vector and copy it to the other side. That should help.
As to the thin layer still showing, try raising the Preview Simulation Quality under the Toolpath menu option.
I laser scan original grips, and reverse engineer the backs to fit the gun. That part is not a problem, the tedious part is to make the front and the back blend into one, and to gauge the final thickness and appearance.
The panels are, of course, different from side to side, but the 2-sided job makes it possible to see how the back cuts line up with the front cut (ie front to back, not left to right). The easiest way to describe the problems I have been having is to think of an irregularly shaped object that you're trying to carve out from the inside in an irregular pattern, only cutting through in the right places and not cutting through where you shouldn't. If you look at the grips in the link I posted, you'll see what I'm talking about. In the past I have used outlines and other "helper vectors" like you describe, but it's still not the same as seeing it in one single simulation. I set them up in pairs and run the backs, then I flip them upside down and left to right (in other words I flip around an y-axis right between the blanks). Some cuts only leave a thin sliver of wood, so I have to index the machine very accurately and I also need very accurate models to work off of. Really, it's more like machining than wood carving.
I'll try the simulation quality next time I'm in the shop, but if it doesn't work I'll simply use the extra perimeter cut in the simulation.