The orange highlight means it is a two-stroke key. You use those to combine the accent with other characters. You press the key, and the accent will print, highlighted in yellow. You then type another key to combine with that accent.
Normally, those are accessed by using the option (alt) key, but it appears those are "hot." They do not need the Option key to activate the combining function.
Now, for it popping up. I had that problem recently when I was playing with other input sources. I never figured out why it was happening, and I wish I could remember how I disabled it. I think I removed the keyboard viewer from the menu. However, I have it back now, and I am not getting those popups.