You did not mention which language you were working in. From the '#', I suspect it was Python.
Note that uncommenting with ^E only works if the line was commented with the same command. By default, Geany comments with `'# ~ '` (you can change that in `Preferences | Editor | Toggle comment marker`). Take care with the ' ' at the end of that field - it's there! Of course '#' is implied - that depends on Python.
So, if you comment with ^E, it inserts `'# ~ '`. If you try to uncomment, that will only work if it finds `'# ~ '` in the line(s).
About the comment formatting - That is a question of taste, I'm afraid...