First, I'm not sure you can annotate a PGN directly. You might need to import it into a database, such as clipbase.
Which version of the program are you on? I'm on 4.15 and can't get the comment window to disappear at all, though you can toggle between showing or not showing the annotation symbols and the board; there are three different options there. You choose those by clicking the down arrow on the bottom of the comment window.
I'm trying to figure out how to annotate a completed chess game. I have the Scidvspc program. First I save the .pgn file there. There is an option under the Window tab called Comment Editor. I believe I got that to work once for adding annotation. But now, instead of the annotation screen, it shows a board with arrows and symbols and such and I can do nothing with it. Anyone know Scid well enough to fix this or do I need another program to annotate games? I'm up for whatever is easiest. Thanks for any insight.