Sniff is a brute force tool, so the combo file it can create is mainly just for looking through to quickly find the graphics you want. Once you find them, you look at the file offset they're at then check in the log file to get the starting address in the ROM for the compressed structure that had those tiles.
At that point, you'd normally use decomp to extract just that structure to a file, edit it, and then you can use recomp to put it back. Although in your case, you may want to copy your already modified tiles into that file from the combo file with your tile editor.
You'll probably also want to compress it to a separate file first just to check if the compressed size is going to be the same size or smaller than the original.