When you say, using a master relay… you mean the stinger, correct? Also, is the general consensus that most/all accessories should be keyed?
Ideally:
Do not connect anything aftermarket to the primary battery (except for a voltmeter). It should be dedicated to starting the machine and running the various factory components that are more sensitive to voltage fluctuations than aftermarket goodies (e.g., the DCT).
All additional accessories should be wired to a fuse box that is energized only when the key is in the ON position. An exception to this would be a winch, as you want to wire that (the big leads) directly to your secondary battery positive and negative cable, and then (likely) the solenoid trigger to a switched 12V supply.
To power the fuse box, you'll install a high amp continuous duty relay (such as the Stinger or, if you live in a colder climate where water freezes, a Cole Hersee relay). Wire that up so that, when you turn the ignition on, it provides power to the fuse box.
Also install a battery isolator, such as the True AM model sold in the club store. The purpose of this is to protect your primary battery from being run down in the event you run your accessories a bunch or which a lot. It monitors the batteries and, if the voltage drops too low in your accessory battery, it cuts the connection between the primary and secondary battery so that the primary is not depleted. Not only can this negatively affect starting the buggy, but it can affect normal operation of the DCT.
Optionally, you can install a switch (sold in the club store as well) that will allow you to energize the fuse box with all your accessories without having the ignition on. It has three positions: Key-on powers the fuse box (aka normal operation), switch on powers the fuse box (irrespective of the key-on position), or OFF. This is great for times you want to run an accessory without having the ignition on, such as playing the radio while hanging out.
Most install a dual voltmeter so that they can monitor the charging condition of each battery, independent of one another. One of the aforementioned True AM isolator kits includes a dual voltmeter. You can wire this so that it turn on either when in the key-on/override position, or (as some have done) add a normally open switch that allows you to check battery voltage by pushing a button. The latter is good because it lets you check voltage even when the machine is off, truly isolation the batteries.
