dont over think it... a standard deep cycle group 24 is more than adequate and light enough for a 12' skiff. bump up to a group 27 or larger if you plan on being out for a long day. I've never needed a boat charging system for my battery. I charge it up at the end of the day in the garage and its good to go next time. don't waste your time with a battery box.. you'll find you'll never put the lid on it cause it knocks the alligator clips off the terminals. I also have a small bilge pump set up on alligator clips that I can hook up in a hurry if I need to.

for an anchor on my 14' skiff, when I'm in salt water, I use a 5 lb danforth with 3' of galvanized lightweight chain and 30' of 5/16 rope... I have a small bow on my boat so I put a roller and cleat to make it easy to raise and drop... (in the salt, i'm never anchoring in more than 10-12' of water)

in fresh water, a milk jug full of rocks and 30' of rope is more than adequate