If both websites are in the same suite, then both domains should be coded into your Internal URL Filters... moving directly from Website A to Website B shouldn't track in your referrers report at all because it should be treated as internal traffic (the same as moving from page a to b within the same site).
If you need to see people moving between sites, if you are tracking the domain in a dimension (like server or a custom prop/eVar) you could use a flow diagram to see movement between the sites.