Linking Strategy

[wryfhk22]

I've always worked on the belief that linking your pages together through a navigation bar would help search engines crawl your site. However i am now working with a client who has a extremely awkward site layout.

A lot of the pages aren't directly linked together (some not at all ). I've got a sitemap with a link to it inside the front page of the site. Will this cause search engines problems and decrease rankings? Or should i just get the moaning site owner to change it around.

Thanks to anyone who can help