big 12 volt power issues

I personally think so!! especially with only a 300/4 and a 250/1 !! I think at peak power even if the alt can't cover the max current demand you wouldn't have full amperage coming only from the back battery I think both's batt's would assist depending on resting voltages. (which should be close to 12.5ish) I think 100amp is plenty. i'm pretty sure at with rough calculations a 500/1 pulls 34.7 amps at 14.4 putting out 500 watts. not including efficiency loses, which are quite bad with the 500/1 and technically the 250/1 compared to other class d amps, I think with 80% efficiency which is high it should've pulled 43 amps so with a 250/1 you'll be pulling quite a bit less than that. one good battery and the stock alt should be more than enough too :) don't think your putting a winch or a snow plow or anything hehe :)

So maybe I should just run the Kinetik battery as my main and loose the two battery configuration all together then?G 35 Driver

Keep the second battery - it is worthwhile and almost essential (and beats a cap!). Keep in mind your original question was about a discharged battery - hence some sort of drain on your system. The isolation relay isolates the main battery from such discharge. Your alternator seems large enough (batteries are not discharging during normal use when charging), so it is a load fault - the amps are staying on, or something else. Tommy's bcae1 references are good and reiterate the basic things that I have said (I add extra detail, and the odd opinion/experience/reality).