Normally accidentals (notated flats or sharps) are entered as the note is entered, by clicking on one of the accidental boxes in addition to the note symbol itself. And if you play on the keyboard a note that is not in the key signature it will automatically appear on the staff with an accidental. But you can also add an accidental to a note that has already been entered by selecting the note and then clicking on the box of the desired accidental.
There are keyboard shortcuts for changing accidentals: the - or + keys will alter the accidentals of a selected note or notes ('-' lowers the pitch, '+' raises it), and if no notes are selected but the cursor displays a note tool then these shortcut keys alter the accidental displayed on the cursor.
The empty box is the default choice if you haven't picked one of the others. It stands for "as this note would be in the current key," that is, no accidental. That is not the same thing as a natural, which always means that the note is a "white key" note on the piano. Click on the empty box when you need to clear an accidental from the cursor, or to change a note in the music from its current state to whatever is appropriate for the key.
A precautionary accidental is one that is not technically necessary but may be desirable for reasons of clarity. Unless you tell it otherwise, Counterpointer will not display a sharp or flat that is already in the key signature. For example, if you enter a flatted E in the key of E flat, Counterpointer will display the note without the flat sign, since that flat is already in the key signature. If you want to override this feature in order to enter a precautionary accidental, hold down the option key as you enter the note with the accidental, or as you change its accidental. That will tell Counterpointer to display the accidental regardless of whether it is required by the key signature.
The marked sharp in measure two, below, is a precautionary accidental:
The screen keyboard (or your MIDI keyboard) will normally play according to the key signature. But you can override these default enharmonic choices. If you hold down the option key as a note is played it will come up as some kind of flat (even if it's a white key), regardless of key signature. If youhold down the command key the note will appear as a sharp (again, even if it's a white key). This feature may be handy in transposition if, for example, you are in a sharp key and want to transpose a passage so that the starting note is E flat.