So that I'm sure I understand, you want your GUI to be drawn in front of the CRT? So not affected by it at all, just a clean GUI over top? If that's the case, then keeping your GUI code in the Draw GUI event should be fine. If it has a pixel aesthetic, then you might have to use display_set_gui_size() to make sure your GUI layer is the size that you expect.
Viewing post in GUI Help
Ah ok. So when you've tried it up until now, did you move all of your Draw GUI code into the Post Draw event, and used crt_draw_begin() and crt_draw_end() BEFORE the crt draw method is called?
If you haven't already, you might try using the GUI demo included the package, and seeing if you can get your game's GUI to work properly there in the example project. That would help figure out where the issue is.
Without any visual to go on, It's difficult for me to diagnose the problem. One possibility that I imagine being pretty common is that your GUI might have been designed for a fullscreen, high resolution frame, and when the crt effect enforces a low resolution your GUI elements might be falling off the page. You could try drawing something super simple in the included GUI example room, like a large circle at [0,0], and then try replicating it in your game. Other things to nail down: Does your game use 3D projections? Viewports?