Pictures?

We need pics and honestly a stone look panel is IMO a rip out issue, painted stone at the best of times is not a good idea and fake stone painted definately not.

This is the dark paneling I am painting over and the stone panels that have to stay. What color should I paint the wood paneling?

If you can, paint over the fake stone too. Don’t try to match it.

I don't get what you're doing or why the fake stone panels have to stay. We need more info to give you better input. Can we see the entire room this "contraption" is in?

So the room has fake wood paneling and fake stone on the walls. That's OK. Lots of us started this way, however, to advise you correctly see need to see the room entirely. What are the floors, how much light do you have in the room? Learn from us.

The paneled walls can be painted if that is the correct solution for the room. Here are some painted wood walls.

To paint paneling, first clean it with TSP (tri-sodium phosphate) rinse, let dry, lightly sand, tack off sanding dust, prime with 2 coats KILZ or Zinsser and then paint with 2 coats of color.

By the looks of it, it’s not real wood paneling, so it just needs to be primed and then painted.

I agree with suedonim75. It appears to be a 'masonite' paneling which is fiberboard and cannot take sanding as the 'wood' is only paper applied.

IMO, take both of them down and if you can't replace expensively, try luan at about 20 per 4 x 8 sheet. Painted, it will look better than what is there.

Ok, so we live in a parsonage that belongs to the church we serve. There is no budget for replacing the paneling. Which is why I am painting over the wood and leaving the rock. It's textured too much to paint. Not trying to match it but find a color to compliment it.

You could paint the paneling the color of the "grout" lines on the stone part.

If it needs to stay, I'd select the lightest off white color in the fake rock.