I did mine myself, and I did not re-install the vinyl top. Depending on how bad the damage actually is and how persnickety you are with the result, you could be looking at anything from a relatively simple repair to a full quarter panel replacement. Has it rusted through? Does water leak into your trunk? Are the bottom edges of the quarter panel also rusting from the inside due to water collecting behind them?
It can be done and you can do it. Time is on your side. The thing about body work is that as long as you take your time and don't get in a rush, it's a skill that can be learned and even if you make a mistake, you can always back up and start over.