A client wants a new domain name for a new subsection of an existing site (very large site with subdomains, etc).
This URL will effectively point to the new section of the site (different URL). The reason they want a separate domain name is branding, nothing to do with keywords (although I've pointed out the benefits).
My question is how best to set up this new domain. I don't want to upset the search engines (esp Google) and I know there are different ways of doing it.
Now I'm not a webmaster and I'm not a techie so if someone can explain in simple terms, the options available, I'd be very glad.
If I understand your question correctly, simply register the new domain name and point it at the new subsection of the site. Insure that the content of this new section isn't duplicated in the old section and that there are a few links (not hundreds!) between the sites and you should have no SE problems.
If the new domain name contains keywords, building this site using absolute addressing (as in "http://www.mysite.com/index.html") instead of relative addressing (as in "./index.html") may help you acquire more prominent listings on some SEs.