If you have the GFX already extracted and is seperated into GFX00.bin and so on and so forth then skip this.
If you dont then go to Lunar Magic and click on the red mushroom at the top and a folder will be created that is named Graphics in your Roms Directory when you open it, if its named AllGFX.bin then go back to Lunar Magic (Delete the AllGFX.bin, you dont need it) and go to Options -> Use Joined GFX Files and uncheck that and then press the red mushroom again then when you go to your Graphics Folder its all seperated.
now what you do is that you have YY-CHR and so open up GFX10.bin in it and you will see the Overworld stuff. so change that to whatever you want.
To get the palette right you will have to go to the overworld in SMW and make a savestate with ZSnes then close ZSnes and when your in YY-CHR go to Palette -> Emulator State Load or press F12 then pick the savestate you just made (Its gonna be a .zst file) and then scroll up or down to get the palette right and there you go.
Edit: If you wanted to change the Land or Layer 1 stuff then open up GFX1C.bin for whats used in Layer 2, GFX1D.bin for the other Layer 2 thing, and GFX1E.bin for the Layer 1 stuff