I have to agree with KellySails. Kremik marina, near Primosten, is a great place from which to depart. Last summer we chartered from Sunsail and they were great. It's less caotic than Split and has good access to either northern or southern bareboating grounds. Similar in size and organization is Sukosan marina, but, it's a bit too north to truly bareboat the best part of the coast - south of Split.
If you want further details, I summarized this as well as three other Croatia trips
(from Sukosan near Zadar and Split) on BareboatingtheWorld.com, my sailing blog. It will give you some insights about bareboating on the Dalmatian Coast for each area including provisioning tips and some restaurant recommendations.
My favorite two experiences -- eating calamari and the Korcula town. Enjoy.