To start off it off I will say I just replaced both my batteries with Interstate green top batteries about 7 months ago that have higher CA and CCAs than the last set of walmart batteries I had. 

Problem is that I got a new(er) truck to drive around for better fuel economy and comfort so now my truck in sig, 2001 ram 2500, is losing charge after sitting for a little while. I actually started to notice prior to getting my new truck about 3 weeks ago that even after it sat over a 2 day weekend it seemed like it took a few more turns to get it to start. This time it sat for about 2 weeks and it was completely dead when I tried to drive it this past Sunday. 

Any guesses on what could be slowly draining the batteries? I do not have any aftermarket accessories running when the truck is off. And besides a regular pioneer radio in the dash that is the only aftermarket interior change which I put in a few years ago. 

You need to pull one fuse at a time and measure the amperage draw one circuit at a time. When you find the circuit with the heavy load you can now isolate the problem. Make sure to remove any accessory connections to the battery directly.