Click on the search function, put in "sharpie ink" and read some of those posts. Lots of products tried to remove ink, seems as tho Mr Clean has some wipes that are effective. Also I have used and tried the hair spray and it takes a lot of stains off vinyl, fabric etc. Good luck!
What color is the stain on the seat? It might not be from your cover but from mold that was in your seat cushion that surfaced to the vinyl do to the heat created by the cover. I have seen this many times. The sun will fade it out and some cleaners will help.
Try using Spray Nine with a Magic Eraser. It usually will bring vinyl seats to a like new condition. Not sure about dye stains though. If it is mold as suggested above, it should kill it.
