(Assuming that the file you have is a GFX##.bin where ## is a hex from 00-33)
Open ROM in Lunar Magic.
In the options menu, make sure that the "Use joined GFX files" is
UNchecked.
Click the Red Mushroom button.
Go to the folder where your ROM is. A new folder called "Graphics" has been created.
BACK UP THIS FOLDER IN CASE OF ERROR.
Copy the new GFX##.bin that you have into the Graphics files, replacing whichever one it would overwrite.
Back in Lunar Magic, click Green Mushroom.
Change levels in LM to reload.
Test.
HUGE EDIT
Unless of course you want to have
multiple character graphics. In which case you will want to use the
Player ExGFX patch in harmony with whatever GFX you have.
Your layout has been removed.