The problem that I have with splitting a party of PC's is the "sitting around waiting for the other group to finish" factor. Sometimes, it can be good thing. Gaming is a social activity, and sometimes lulls in a game allow your players to get some non-gaming social contact. However, if this goes on to long, players can get annoyed, distracted, and even unhappy. Going "out of game" can ruin the narrative feeling of a session.
If I was going to split the party as regular thing in a HQ campaign, I would institute some kind of troupe style play in which each player would control one or more followers of another character. Hopefully, this would allow all of the players to be involved in some aspect, albiet small, in most of the scenes, and keep the players "in game" as much as possible.
-Santo
"Aum Shanti Shanti Shantih."
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