My main initial concern is creating the theme to make wp look just like just another page on my site. I've read through the theme development page http://codex.wordpress.org/Theme_Development
and it mentions get_sidebar() to use sidebar.php which I can use for the right hand column but I'm unsure how I go about pulling up the code for my left hand navigation column. I'd appreciate any advice.
Also any general advice about how difficult migrating my site design is likely to be, from those with experience of such matters, would be very helpful.