Another WordPress Skins question…

So, up until today, I was a faithful Greymatter user; I had used it for years and was absolutely happy. But then this afternoon Greymatter decided to die inexplicably, and I’ve spent the past three hours grudgingly installing WordPress and scouring the codex and these support topics to find a way to integrate it into my site.
My site is written in php dynamic includes — meaning that my pages load in “index.php?o=blah&x=blah” format and “skinned” — meaning that I have 4 different layouts visitors can choose from, when they select one a cookie is made so that their browser remembers which one they have chosen and they don’t have to change it each time.
With greymatter, all I had to do was take out any kind of styles it was incorporating (therefore leaving a non-designed plain .php file) and include it by linking to the index file through this format: index.php?x=greymatter.
I’ve created basically a blank template for WordPress, which uses no CSS in the actual template so that each skin’s CSS will override. That worked fine, and I’m sure it’s exactly what I need right now.
There’s only one problem (and this is where I could get confusing). When I go to the page where WordPress’s index.php file should show (index.php?o=blog, because variable o designates the directory and variable x defaults to index if not designed) it either obliterates my right-hand sidebar (I have one on each side) or doesn’t show the WordPress content at all, depending on what I put for “define(‘WP_USE_THEMES’, false); ” in the WP index.php file. If it’s false, WP doesn’t show up. If it’s true, my sidebar is gone.
Is there a way to create some kind of harmony? Why can’t they get along? Why not both?
Any ideas?
[Page in question: https://www.hello-toby.com/?o=blog ]