while i do have two panels i as planning on only using one of them and it sounds like that is all the MPPT can handle.
No. You might want to read the answers again. Your 20A MPPT won't handle even one of those two big panels. "Some" MPPT can handle much more than they are rated for (or claim so), but without any information about your MPPT it should be assumed that it can't.
seems like i need a 45 amp PWm
More like 25A PWM (for 360W of 12V panels). Panels have to be of the same wattage, or very close.
for the larger higher voltage 335 watt 40 volt panel I need an additional 30 or maybe a 40 amp mppt controller when when i use that panel.
Still want to do it the hard way, eh? :) You don't mix PWM and MPPT, there is no need to, it complicates things. As said before, if you want more watts - get a few big 24V panels and one big MPPT.
I was looking at the bogart 2030 charge controller but it only go to 30 amps which would not be a problem now but woiuld be limiting in the future if i decided to add another panel or two.
Not really. For 360W array of 12V panels you need 25-30A controller. Bogart will do. Also, Bogart is one of those PWM that do allow higher wattage without going up in smoke. With a bigger 500W array it will still limit the output to 30A, yes, but you will rarely get 30A even with 500W. Keep in mind that Bogart controller is an add-on. It won't work well unless you couple it with Bogart battery maintainer, and this one would cost more than the controller.
the Mppt I am looking at is on amazon EPEVER 40A MPPT with remote and temp sensor cable.
I doubt that $150 will buy you a decent 40A MPPT. Though, EP Solar aka Tracer have been around for a while and cobbled up many models. With varying specs on the same model, depending (probably) on which factory printed it.
You don't really need MPPT with 12V array. Bogart will do fine for 400-500W, and will kind of forcefully make you aware of your battery charging state, which is something that you might find useful.
Alternatively, Grape Solar 40A PWM will suit your needs fine.
PS: BFL is right, for a pair of 6V batteries you don't need a lot of solar. Get 3*120W or 4*120W in parallel and $50 Grape Solar PWM, he's a good one.
