Best thing I've found for full Citra compatibility. This is what I've been using to play until official full screen is implemented. This program is 100% free and does not use any zoom function. Instead, it removes title bars and maximized the form window. If you disable Single windowed mode, load up this program, and set the game window to full screen (F3), it will remove the title bar and scale the game window to your monitor. Here is a screen shot
I use the single screen setting in Citra and toggle between the bottom screen with my controller's left stick click (PS4 touch pad to simulate stylus). I accomplish this by using steam to launch Citra and button map my PS4 controller; however, the same thing can be done with alternative software such as xpadder or using your keyboard every time to toggle swap screen (if you're a masochist). Hope this helps anyone else in the same boat as I found myself!