vBulletin 3's layout is built using tables that are controlled via CSS.
Whenever I want to edit my forums to look exactly like my site I edit the header and footer templates, since they are globally generated in every page of vBulletin.
Hope it helps.
And if that doesn't help you can try editing every template that is in all caps (eg. FORUMHOME, SHOWTHREAD, etc...) and putting your sites code in those, since those are the main bodies of the different pages.
I tried my best to explain but I'm sure I didn't do very good. =/
Yes that will help out alot... Thanks Ryan. Though I haven't gone back there yet, there is no need to edit the 'child' templates? (ie FORUMHOME).
I also want to edit pages like Activate Your Account, Email Activation Codes... all that are NOT general pages.