How hard is it to
 

I need to basically reskin the WHOLE entire cart to look exactly like our website. After reading some of the editing guides it seems if I edit half the pages to correspond with our site, the admin side of the template will not work at all?

Re: How hard is it to
 

Not true, you just need to be careful with the shared templates like dialog.tpl and menu.tpl. The admin side has its own default css file and template, just some things that are shared.