I am not entirely sure what you're talking about. Could you post an example?
Usually these things are done by going to your layout tab in your comic options and clicking on raw html. You should then be able to find where you want the code to go because it is pretty well marked with descriptions. Just copy and paste the code where you want it. That is assuming you are copying this code from somewhere.
You know, like Polldaddy. But polldaddy is too limited. I just want a way to tally up votes. I want to be able to allow my readers to vote on what happens next. Sorta like majority win "choose your own adventure".
..............................click this one............................................................or this one
They're both cool as hell