I basically remove as much of the natural free edge as poss, then apply my tip. Generally I cut out the pre cut wells to make them smaller so there is very little contact area. I pre blend natural tips by buffing over the well to reduce the thickness as much as possible so that when it comes to blending on the nail there is very little left to do.
I have several different types of tips with varying degees of c-curve so that I can tailor it to a flat nail plate, a curved one, or one with deep side walls. Like Scattyfox says, it will come with time. My tip fitting used to be crap, but now it's all but spot on every time. If you are having to push a tip down to be flat on the nail plate then it is too curved, if you don't have a variety of tips like me then you can go up a couple of sizes and then tailor the sides with your file to make sure they are flush with the natural nail.
Learning to be a good nail technician takes patience and practice so try and take it one step at a time and not to be in such a hurry - you'll get there!