I have 2 batteries in the bed of my truck. I run a battery isolator to charge them up because they are deep cycles. You should only charge your second battery off of your main battery if they are the same battery. If they are different, they will drain each other. A battery isolator is the best route to go if you are using your second battery for accesories like power invertors, winches, ect... A kill switch for your second battery is always good to have on board as well.
If you can put a second one under your hood, I highly recommend it. This involves removing the airfilter box. I've heard that you can take the 2nd battery box off of the CTD and install it there. If not, be prepaired to dump some money into the appropriate cabling to make it to the bed or to a battery box attatched to the frame.
Just curious, what are you wanting to do with a second battery?
Basically, you have to get a new intake or make your own. The airfilter box has to be completely removed to get the other battery in there. Problem is that most aftermarket intakes run through this area. That is the big reasons I don't have one up there. There are a couple of the cheap intakes on eBay that put the filters above the engine. You could also just purchase the individual pipes and piece something together that routes around your battery... or get a shaker hood