Do you mean if you put the code into the textarea itself?
Or do you want something like a link that is placed in the textarea to become html code.
For example, I once made this plugin ask people to paste a link to their blog into a text area.
Obviously I didn't want to hand code each link that someone sent to me into something clickable before putting it into my blog, so within the "Message Body" (the part that is supposed to be emailed to me) I put the html around the short code. This way when I received the message the link in an email it was already coded. Does that makes sense?
If not, I'll send you a screen shot.