As long as you're working with multiples of 8 (8, 16, 32, 128, 640, etc) when you build a tileset in the program, the engine will be fine. There are a couple restrictions, like diagonal wall tiles have to be square. That said, the engine right now expects the player sprite to be about 16x24, give or take a couple pixels, and items (pickups and stuff) all have to be 16x16.
Since you build each tileset yourself in the program, it doesn't matter where the tiles are in the set, or how large they are, since you'll be telling the engine that as you build.
You did see this tutorial, right?:
https://youtu.be/bC0IScIohjA