I can't play and use red helper at the same time

what is red helper?

If you use emulator you should use the emulator called BGB. There you can enable the hot keys, so when you click out to use red helper, the emulator will not get paused and you can continue playing while you check the red helper.

screenshot of my desktop while playing. Gambatte reads input when it's in background, so does the timer.

I actually made the timer a bit slimmer and the gamescreen bigger later on