Hi xbrunox,
Your setup is extremely unusual.
With GM, you can't use video bgfx and monitor custom. You must use video auto (= video d3d) which means D3D9ex. Then, if you want all games in their native orientation (so they output fine on both CRTs), you need -orientation rotate_r, or -orientation rotate_l, depending on how your vertical CRT has been mounted.
With regards to your LCD, you need to find a way to enable bgfx just for it, as long as you use it as single monitor. It's not going to work in a multimonitor setup, e.g. LCD bgfx + CRT d3d. As said, LCD bgfx + CRT bgfx will break GM as bgfx can't switch resolutions in current implementation.
So basically you'd need to create specific inis for games that you want to run on the LCD with bgfx shaders. Not very handy but please understand that GM was never created with such setup in mind.
We're working on a new Switchres interface that will be more flexible for multi-monitor setups.