As everyone else has stated, connected realms are meant to be seamless in the sense that everything is "merged" except for players and their names. (Not entirely sure how guilds names are handled, though)

Quote Originally Posted by TheOlz View Post
Also, anything multibox specific that might be a limitation?
I tested Jamba and isBoxer quickly and didn't have any issues (just remembering that "name"-"server" is needed), but it wasn't a thorough test, only about 10 mins.
If your ISBoxer is up-to-date (Help > About), then you should see a separate Game Server Name field below the Actual Character Name. This alleviates the need to use character-name under Actual Character Name and fixes the issues that are introduced when running a few characters from the same realm and different realms.