Hi,
Your post is a few months old, so I'm not sure if you still need the help. I've worked on 6 webjobs sites to date, mostly because I figured out how to use it and other people found me. My company is
http://www.globalrepresentation.com, which is a really highly customized webjobs site. I've also worked heavily on webjobs for
http://www.himconnections.com and
http://www.utilityjobsonline.com among others.
For modifying the templates, you'll need to mostly modify the templates/page_top.html and templates/page_bottom.html files, along with the career_style stylesheet. Depending on your design, you may also have to modify each individual page template because webscribble has table sizes inserted in there. You'll also need to modify all of the templates that serve up the different navigation bars -- off the top of my head I think they are called find_jobs, post_jobs, etc. They aren't completely obvious but a search and replace in Dreamweaver or your editing software can find them. One issue is that you can't change the page_top template for each page. If any page uses a different template you'll have to detach it from the webjobs system. Or at least I haven't found a way to serve up a different page_top, and Webscribble states it can't be done.
If you still need help, feel free to email me. I have a few webjobs hacks posted on
http://lifehackmom.com as well.
Jen