It's unfortunate you didn't find this forum before improperly installing the flange. I suppose you now know why a flange is supposed to be set on top of the finished floor. At this point, shimming is about the only option you have. From your description it sounds like the floor is level so the toilet is 1/4" above the floor all the way around, but if that is not the case, then shim the toilet to level. You want to put shims in several locations around the entire toilet so that the weight of the toilet and occupant is not on the flange alone. You must keep the toilet from having any rocking movement whatsoever or the wax ring seal will break. Trim the shims even with the bowl then caulk around the toilet base. The flange bolts should not be tightened more than just snug. Their purpose is to simply hold toilet from rocking. Too tight and you run the risk of pulling them out of the flange, breaking them, or breaking the toilet. I think shimming under the flange would be a good idea too since it is now just supported by the connection to the drain. You might use some marine plywood with a hole cut to the size of the flange pipe, then cut it in half so you can slide the two pieces under the flange. The flange should be anchored to the concrete floor in several places as well.
Some of the pros might have some other suggestions that would work better.