I have two existing visa exempt entries, one was extended by 30 days.

Also have a SETV that was used this year and extended.

I am on my second SETV issued the beginning of this month. I left Thailand last week for a few days after getting a re-entry permit. I am planning on leaving once or twice again over the next month. Should I keep getting re-entry permits? I don't want too many visa exempt entries and get flagged at the airport.

The type of visa exempt entries are more important than the total number. Getting them back to back can be a problem. It also depends upon whether you are entering overland or by air. If two are all you have and it appears you have not been doing them back and have used tourist visa you should be safe getting a couple more of them.

Whether you want to get additional re-entry depends entirely on the amount of remaining days you have left from the 60 day entry and whether you plan on getting a 30 day extension or not.