So, it's actually quite simple: I use a program called LibreSprite. It’s open-source and free. You can download it here: https://github.com/LibreSprite/LibreSprite?tab=readme-ov-file.
Once you have installed the program, you can open a sample spritesheet. I’m not sure how it works in Godot, but in RPG Maker, I copied the example tileset and opened it in the program. Keep in mind that RPG Maker uses a 48x48 grid.
Then, I opened the city tileset in another window, copied the buildings I needed, and pasted them into the previously emptied example sheet.
In RPG Maker, the image is split in the middle, and the right half is placed below the left half. I’m not sure how it works in Godot.
If you have any questions, I have sent you a friend request—feel free to send me a message.
I apologize for the delay; I was very busy.
On the other hand, you’ve made me curious: What kind of game are you developing? (You don’t have to tell me if you don’t want to, but I’d love to know!)
I wish you lots of fun with your project!