I wouldn't have to worry about doing visa runs every 3 months.
The good news is that you will not have to worry about doing visa runs every three months. The bad news is that you will not have to worry about doing visa runs every three months because you simply cannot do visa runs any more; once you have been here for 90 days, you then need to leave the Schengen zone for at least 90 days if you do not have a residency permit.