A lot of hi-buck RV rigs use the same charging setup that Jake mentioned.
I've read the same stuff about deep cycle batteries needing different charging than starting batteries. As I understand it, starting batteries are meant to pump out a big surge of power to start the engine then be recharged quickly. Deep cycle batteries are built to output a little juice for a long period then be recharged for extended periods because they've usually been drawn down by 50% or more and need a lot more juice to recharge.
The main problem with charging starting and deep cycle batteries together is that the deep cycle bank can keep the alternator at peak output for a much longer time which can do two potentially nasty things: First, alternators aren't designed to work at full output for extended periods and (may) burn their windings out, particularly if the alt is kinda small to begin with. The second problem is that the starting batteries can become over charged and boil out a lot of battery water before the house bank gets a full charge.
If both the starting and house banks haven't been discharged much, the alternator will do fine but if there's a big difference in charge states there could be trouble. The best way is to charge starting batts. with the alternator and charge the house battery with a good three stage battery charger. If you have access to shore power when parked charging them separately isn't too much of a problem.
That said, I have our banks cabled together so I can use either charging method in a pinch if needed, but I do try to charge the banks separately.
The Progressive Dynamics line has some nice chargers. http://www.boatandrvaccessories.com/bb0 ... s&kw=bb074