Sites of companies that do web design should be submitted only once, in the most appropriate Web-Design category. Mention the other activities in your proposed description. This is a strict guideline, since basically all web design offer some combination of related services.
As a completely separate issue, if the company has a local presence -- if they meet with clients face to face all across southern metropolitan Podunk, New Jersey -- then you can submit to the Locality category (under Regional) where the main office is.