Hey guys- New boat needs to have a little bit of glass work done over a decent sized area (2'x2'). The area needing work has fresh bottom paint over it. Does the bottom paint need to be stripped completely off before I can do the work or am I ok sanding it down some and then going over the top of it?

You want fiberglass to fiberglass bond not fiberglass to paint. Take it down to raw glass a scuff it good with some 50 grit . I would also heat it up before you patch it with a light bulb or a heat gun. Not to hot just warm