AutumnDay
You're actually doing what you should be doing.
Just like when learning the staff, you marked up the sheet in the areas you didn't know or were unsure of. You eventually quit as you got more familiar with what notes are on what ledger lines.
So too will you do the same for sharps/flats.
Pay attention to learning the various scales AND their key signature markings at the start of the score. Test yourself; play the scale for whatever #'s or b's are in the key signature. For instance, what scale would you play in a piece with ## as the key signature? What keys are sharp, if any?
Say the notes in the scale, play them on the keyboard. Do this for every new piece you play at the very beginning of practicing it.