I just replaced the flapper on my toilet, yet it is still running through the hole. I feel like it has something to do with the seal. What should I try next?

There are several things you can check.
1-make sure that you have a quarter inch of play in the flapper linkage.
2-Run your fingernail around the seat. If you feel nicks or rough spots the flush valve must be replaced. Let me know what you find. Good luck, Tom