It may vary by airline, but in general, you can check in online and then still check a bag at the airport.

But the main advantages IMO to online checkin are (1) no need to visit the counter, and (2) you can miss the checkin cutoff by a couple of minutes and still get on your flight. Having a bag to check negates both of these. So it probably doesn't matter much.

If you do miss your domestic flight by two hours or less, most airlines will allow you to fly as a standby on the next later flight. It's sometimes referred to as the "flat tire rule". In that case, an online checkin may help, since some airlines order the standby list (within elite groups) using checkin time.