I had one !12 volt in a class C removed it and added two 6 volt and a 1800 watt Xantrex inverter,I can bring the batteriesall the way up and in two to three hours there completely down.Could it have something to do with an isolator?

Well somethings wrong for sure. Where did you get the 6V's at and what brand are they? Are they both the same make/model? What are you powering during the discharge cycle? Possibly a loose connection somewhere causing high resistance to the circuit.

How long are you charging?

Batteries are from Sams Club ,Iwas told made by Interstate

Originally charged for atleast 24hrs I am just not pulling that much to suck them down that quick.

I forgot to ask at what rate of charge too? Example- 24 hours with a 10 amp charger may not fully charge large batteries. If its not a full charge, even though the batts read as 13v, it may only be a surface charge, not really fully charged.

Also, deep cycles get better after they are cycles a few times...

Get a volt meter from Radio Shack, Harbor Freight if you have to. Charge the batteries to what you think is "charged". Immediately after charging, disconnect them from everything. One hour after you have stopped charging and the batts haven't been connected to anything, read the voltage. You should see 12.6-12.9. If you see less than that, the batts are not charging fully.

I'll try that...Thanks!

How much draw are you putting on your batts?

You have a 1800 Watt inverter, if you're using half of the rated output of that inverter to run stuff off the batteries then you're pulling around 82.5 amps (estimating 10 percent inefficiency). If you have two 6 volt batteries rated at 220Ah, then you'll be run flat in 2 hours and 40 minutes.

If you do have an isolator installed between your charging line and the batteries could be your problem. Isolators are not very efficient and will not allow a full charge to your batteries. Not sure why you would need an Isolator? Replace the Isolator with an Integrator instead, I think camping world sells them. Try their website.

I replaced two 12Volts with two 6Volts in my Weekend Warrior and no matter how long I tried to charge them I could never get them fully charged (per the monitor) but I never had an issue with them running down either.

Have you checked the water levels?