How would I keep tile ids consistent when importing multiple .pngs?

That title was a mouthful. Okay, here is my problem.

I have a sprite sheet of 16x16 tiles I use. I also have a series metatiles (i.e. a tile made up of the 16x16 tiles that depicts a small area) saved in as a series of .pngs files. As each of these metatiles does not use every tile in my tile sheet, my tile ids when exporting the png metatiles as a tilemap are not consistent.

I need to take the tileset as defined in my tileset image and make that the tileset that each imported .png uses.

Is this even possible?

Thanks in advance for any help.
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