You will need a charge protection circuit regardless of the use a picoPSU. A picopsu is an excellent solution to to power for the dreamcast, and if you can get one cheaply I would recommend using one. Much cleaner than a string of regulators. I do have a couple picoPSUs sitting around, should you be interested in purchasing one, simply PM me. As for the pinout, most use standard ATX 24 pin molex connectors, so this should help.
And charging should be done with a smart charger and a protection circuit. The ones from batteryspace are quite excellent.