Are you talking about using the Flow Visualization in Workspace, as well as the Next/Previous Page panel?
Then yes, those visualizations should work if everything is in the same suite (I say "should" only because I don't know if there are other odd "in the middle" items in your site flows... (for instance, if you click on a link on Site A, before it goes to Site B maybe it hits Site C temporarily, then is auto redirected to Site B... this can cause issues sometimes because A to C is considered an exit link, and C to B is considered a Referral)
The main recommendation from Adobe is to use a Global Suite and create Virtual Suites from that for each site...
This does mean that all domains must be coded as "Internal URLs" - so if you are tracking referrals from Site A to Site B, this will no longer work... you will need to come up with a custom solution to track internal linkages.
