Wheels use the 'Clear Logos' so you could replace the images in the folder with the ones you wish to use instead and the fact the file names match your ROMs already is great, I would how ever make a backup of your clear logos as you might decide to use them instead in the future.
As with the custom backgrounds you could try adding a image to the 'Fan Art' folder. I've not tryed this so maybe someone that has could let you know as you may need to turn off / on something in the options