Hello and Here are MY answers for the questions you have asked and are IMO. My first question is how many fuses should I run throughout setup? No fuse from batt to batt, you can if you'd like for extra safety, Also, if not already, I would recommend matching batteries. You will then want to fuse from batt to amp(s). If you are going to use a D-block, you want to fuse both leads from DB that Distrubute to the amp(s). So that will be 3 fuses in my setup. should I run this 18" from the battery {front duralast, or trunk yellow top}, or should I run a 200amp ANL at each battery? answered above distribution block, should this be fused? Answered above If so how big of a fuse for the AB output, how big for the 4 channel output? Check for manufactures specs Should the capacitor be fused also? Remove Cap Should I upgrade the big 3 to 1/0 gauged as well? yes The wire I am looking to buy is http://www.wireandsu...0-fslash-01.htm , will this do or should I step up to http://www.wireandsu...0-fslash-01.htm ? I would recommend visiting weldingsupply.com, if your on a budget, I would ebay any 0gauge wire kit. High output Alt- Is 200amp enough or should I go bigger? For your equipment, yes, if you are going to upgrade your system in the future, I would recommend buying the most of what you can afford. Take a look at mechman/dc-alt(not a fan)/singer alternator/ohio generators Power/Ground Wire weldingsupply.com (search "cable") Fuses I have always like the fuses that come with AudioPipe equipment Wire Connectors Take a few looks at this thread Distribution Block Darvex.com has some nice ones Hopes that helps man. LMK if you have any other questions