Once your schedule is created, there are a few ways to change which course and/or side you're playing for a given round:
Go to League Setup -> Scheduling -> Edit Schedule for a Single round. Choose your round to change, and you can select the course, side, and round type for the round.
Go to League Setup -> Scheduling -> Change Course, Side, or Round Type For All Rounds.
If you've accidentally entered scores on the wrong course or side because your schedule wasn't set properly, you can move the scores to the correct course/side. Go to Weekly Administration -> Move Scores to Another Course/Side. Choose your round to change, then select the new course and side. Because scores have already been entered for the round you choose, after moving this will clear out any points and recalculate handicaps for your league. You'll then need to Record Points again for this round since the results may have changed.