You can modify nametables in NES Screen Tool.
Export your nametable for any scene from the Mesen emulator's Memory Tools.
Here I am looking at Nametable RAM, including what looks like the palettes at bottom. Save the nametable RAM as a file.
Open this up in a hex editor. It's twice as big as it should be. Delete the second half of the file from 400 onward. Rename to .NAM.
Import CHR graphics into shiru's NES Screen Tool. Open your NAM file.https://shiru.untergrund.net/software.shtml
Recreate your palettes manually I guess.
At this point you can alter your background sprites and palettes, and save the results to be copy/pasted back into the ROM later. You can also create onscreen sprite displays as a metasprite bank.
You can use NES Screen Tool like a drawing tool here, placing tiles and palettes. Check or uncheck "Apply Tiles" and "Apply Palettes."
The .bin data you save when you're done can be manually reinserted into your NES ROM in the appropriate places.
In Mesen (or in your old DMP file), copy a few bytes/numbers from the unaltered nametable and search for THAT in the NES file.
Find this data inside the original ROM in a hex editor.
(Either in a Hex editor or in FCEUX's Hex editor. Open up Debug/Hex editor/ROM file, you will be able to see your changes in real time. I suppose Mesen can do this too.)
You have found the Nametable for this scene inside the ROM.
You may be able to simply copy/paste your new/altered Nametable info directly into the ROM (from the .BIN file you exported from NES Screen Tool, or from an .MSB if you were working with sprites).
However, the code in the actual ROM may be different and more complex than that - there may be extra commands which jump around the screen, like maybe a three-byte command on every line break, or commands which seek to a specific point onscreen.
So you may need to make changes to your code to account for that.. Compare your new code to the old hex code.
Try this in FCEUX's hex editor, while working with the CHR ROM. See if you're breaking the code by pasting in the new code.
(It depends on the ROM!
They often have some extra code which you have to work around, in the actual Nametables.
Maybe an extra three bytes before every line of sprites, and an extra three bytes in the middle of the color palette at the end.
It's not too hard though! Just something to look out for, and add to your new code!)