I am setting a toilet on a tile floor. In the past I have used two wax seals, one with the flange and one without. The standard size does not seem to seal to the toilet base. How high should the wax extend above the floor and can I use two seals with the flange?

There's a problem with double sealing a toilet. Unless you bevel the wax outward it can spread inward and impede the flush action. You have failed to inform us how much lower the flange sets under the floor line so it makes it difficult to answer your question. Rather then a double seal I would use a wax seal with a funnel. Regards, Tom