Depends on how serious you need to be.
For critical apps, I use this one.
http://www.batterystuff.com/battery-chargers/12-volt/gel-cell/GU16202.html
The nice parts of it, are the fact that it can be left on indefinitely. Won't boil the battery dry. Plus you can select what type of battery you want to charge on each output.
The two outputs are isolated. Each battery gets what it needs despite what the other one is drawing.
I have mine hooked to my genset. Its a 24V system, which means the positive of one bank is hooked to the negative of the other and it does not care.
Not sure if it could do the same for parallel connected batteries though. You might be better off with a three stage single unless you are going to disconnect them from each other except when needed.
I also have a three bank version that is mounted in my tractor barn.
Each output goes to a different vehicle. One to my riding lawn mower, one to my tractor, and one to my travel trailer.
At least they did. Lightning got it last year, and I have not replaced it yet.
When I do, I am going to make sure I have a common earth ground between the units.
It was a cheaper brand, might have contributed to the damage....