The trans holds about 4.5 qts after a pan drop and filter change. 9 qts maybe if the torque converter is also emptied (I don't even know if it has a drain plug, like the V8's do).
Note: If the torque converter was emptied/replaced by the mechanic, he should have refilled it after rebuilding the trans. If it's empty, the trans pump will refill it when the engine is started, then maybe round 9 qts total would be about right. I prefer to fill the torque converter with at least a couple of quarts before reinstalling it. That way you're not running it dry until the trans pump refills it. There's no magic number as to the number of qts you put in as long as when you're done the correct level is achieved on the dip stick. Your owners manual will give you the capacity.
If you've put in 6 qts and the t/c is full, you could drain out about a qt and 1/2 (with a piece of plastic tubing you should be able to siphon/suck it out through the dip stick tube, but it will take you a while. If the torque converter was empty, run the engine for a minute, then recheck the fluid level. Then add or remove fluid as necessary.
It is not normally necessary to have the engine running when you fill the trans, it may even be harmful.
To check the trans fluid level: Vehicle on level ground, start engine and put the trans through all the gears, then check the level in PARK. If the fluid is already warm it should be at the near MAX mark, if it's cold it can be around the middle or MIN mark on the dip stick.
As I recall, when I did mine last summer, it took between 4.5-5 qts of Mercon V ATF to fill it after a pan drop and filter change. Before I started my dip stick registered as FULL. After draining I measured how much came out and that's what I put back in.