It will vary based on the situation.
Some examples:
Some still have minor league teams with too many players. In that case, I will try to shuffle players between levels. If that's not possible, I will release players.
If a 40 man roster is missing players at a certain position, I will try to shuffle the roster around to meet the rules. If not, I'll have to add somebody to the 40 man from the minors.
Anything I do will be done with the intention of keeping the team in the best possible shape for a replacement in case the GM quits or is removed.