Here at Hartge's what we use - if it's varnish and not cetol - is a piece of plexi-glass which we've cut to a sharp edge. Many times we can chisel the varnish off of the gel coat. Of course, if the gel-coat is chalky, it is somewhat porous and the varnish will absorb into it somewhat. Sometimes, with a lot of patience, you can use an alcohol soaked rag - not the rum you're sipping - denatured alcohol - and hold it over the stains - sometimes this will soften the varnish - if it hasn't been down there for too many years. Then you can scrape it up with the plexiglass. The plexiglass if you're gentle, shouldn't scratch the gelcoat because the gelcoat is harder than the plexi.
This is why we always tape out everything - even when we're just sanding. When you're sanding, even by hand, you inevitably sand the gelcoat - it opens the surface and then dirt will get in and discolor.
BTW - you mentioned waxing the deck before applying cetol to the wood. Clean the wood well with Comet or Ajax before starting on your cetol job.
I wouldn't bother with the clear gloss coat - the new natural teak cetol works great if you just put down three coats - nice color and almost a gloss look to it. If you put the clear on, next year you'll have to sand hard before putting on another coat. Without the clear gloss, you can just tape, scuff it out with a 3m Scotchbright pad, clean up with alcohol and put down another coat of Cetol.
Good luck - and remember to take her out sailing once in awhile - unforttunately we seem to work on our boats more than we sail them.