Per instructions that came with Argofet battery isolator. I ran a wire from the alternator output to the isolator. What was not clear in the instructions is, should the old (original) output wire be disconnected from the alternator, or, remain connected. Thanks for any assistance with this.
Yes, assuming the original output wire connects to your starter battery. Disconnect it from the alternator and connect it to one of the argofet outputs. The other output connects to your house bank.
Thank you.
Your alternator was originally connected to the starter as that's the closest (and chunky) connection to the starter battery. The only cable connected to the alternator output should be to the argofet input. One of the argofet outputs will go to your leisure batteries, and the other to your starter battery. Since you already have an existing cable connected to the starter battery (alternator to starter) you could use that as the argofet starter battery output to make life easier. So in answer to your question, yes :)
To be specific, the one alternator output wire goes to the Argo fet input. The old alternator output wires were extended, and connected to the Argo fet output of the starting battery.
Any suggestions you may have to correct this would be much appreciated. I need the ability to turn the batteries off. Thank you.
Could you draw a diagram of your setup (including any switches) and/or take some photos of the back of the alternator? The smaller green wire usually runs to the charging warning light to excite the alternator when the ignition is on, but colours vary from install to install. That one should stay as is.
I wonder if you have a 1/2/both switch that is connecting the battery positives together? These were common in installations before split charge relays/FETs came in. When I redid my setup I had to replace it with separate isolator switches for the starter and house batteries, as the argofet is the only device that should be connecting the positives together.
Knowing this, do you still need photos?
Thank you.
Understood. I would lose the 1-2-both switch if I were you, as the argofet does its job to combine the batteries when charging. You could include a single switch between the two battery positives if you ever needed the house batteries to jump start, though with lithium batteries the high currents from cranking the engine could cause the BMS to trip. In that case maybe keeping a small mains charger on hand to top up the starter battery would be a better idea.
Thank you. I am now on dual circuit for batteries. Lithium batteries only power distribution panel. Starting battery only powers starter. Much cleaner setup. 
White wire from harness to solenoid, small nut. Red fused wore from harness to solenoid, big nut. Another fused red wire from solenoid, big nut, to distribution panel. Lastly large reg from starter solenoid to battery switdh
Thank you. This is for a battery conversion/upgrade on a 45 year old sailboat. From alternator to batteries/isolator requires 18' of wire, so I wanted to be sure. Thank you for your very helpful response.
One more view starter solenoid 
