Hi Jack,
First of all, thanks for being both the first purchaser and the first poster of this tool. I feel like you should get your name in the credits or a special art request :D
If I'm understanding you correctly, you should be able to clean up and partially delete tiles on a layer. You can switch back and forth between adding and removing tiles using the buttons, or the plus and minus keys on your keyboard to switch between add/delete mode. In the next release (coming soon) I have also made some quality-of-life improvements to tool switching in general. One of those is that right clicking will now also switch between add and remove mode.
Here's a gif of how to do it. If I'm misunderstanding what you're trying to do, please let me know!
