I'm sure this has been asked but not having luck finding the answer. So, a game I payed $10 for has a bonus edition for $25. I would like the bonuses, so do I pay the $15 difference and the total gets me access to the higher tier? Or do I have to pay $25 on top of the $10 I already payed?

Unfortunately at this point it's not possible to pay just the difference, you'd have to buy for the full price again.

Just to add to above, if you end up re-purchasing something we can always process a refund on your first purchase. You can contact support to request a refund here: https://itch.io/support