You can get an idea of how tall the wax needs to be next time you pull the toilet...put a straight-edge across the bottom and measure up into the well around the horn. When you set the toilet down on the wax, you should have to push on it to mold the wax to make the seal. If there's little resistance, you have a problem. IF the flange is not level, that can increase the amount of wax needed. If you stack two wax rings, use one with a horn on top and a plain one on the bottom. The horn then helps to prevent the bottom wax from being pushed into the opening and keeps the two aligned.
You don't get two chances with wax...you can only press down, you can't lift or try to move it. The wax isn't a spring, you'll leave gaps. Same thing if the toilet rocks...when one side goes down, it compresses the wax, and when it rocks back, there's a gap.
Typically, the horn of the toilet directs the waste down the center of the drain. Usually, the only time you get a leak there is if the thing is misaligned, or there's a backup. While the wax should prevent waste leaking, it's normal job is to prevent sewer gases leaking out.
It's still possible that the toilet is defective and it won't matter what you do with the seal...it will still leak.