What is the relative height of the flange verses the finished floor? Flanges are designed to fit on top of the finished floor. If it is too low, then you need to accommodate that fact. Get two wax rings: one with a funnel, one without. Stack them together with the one with the funnel on top. That will help to keep the wax from the lower one from squishing into the throat of the drain. But, first, set the toilet down without the wax, check that it sets flat without rocking. If it rocks, it will open up the seal...it would need shims to keep it from rocking. Locate where those need to be, then set the wax and put the toilet on it. You should feel the wax squish as you push it down and it must be stable once it is all the way down.