Okay, I think I got it all figured out but my content. The box thing seemed to be a misunderstanding on my part.
Looking through the manual file the $counter var is not in it, but it is on the weblink I gave. Outdated, maybe?
I have product_info.php which I used all of the tags from the supplied product_info file that came with STS, and just my HTML. All of the text is showing, but none of my html is.
Basically, with my layout, I used divlayers. I have a layer box at the top of the content for the titles/product names/etc and then a larger box below that for the rest of the content, so I figured I needed to do a custom layout for this to make it function properly.
Sorry for double posting, my edit button seems to have vanished.