Yes, that is how I tested the jumper, with the aux (ESS) negative disconnected. ESS still works like this unless you disable it, everything is just running on one battery like the Cherokee's do. Realize that the two battery system is probably designed to fix issues with the single battery system while introducing it's own problems.I carry the fused jumper in my glove box and have wing nuts to install I also put my JL on a Deltran Tender Plus once a month for 24-36 hrs, it’s usually a solid green in less than 18 hrs but I leave.
Normally coming off the tender my batteries are in the 13.2 range so when starting the EVIC display shows 12.7 as the alternator is not putting out that much but within 24-36 of sitting it normally shows 13.5 but if I take it on a long drive it will slowly creep down toward 12.8-13, I keep ESS bypassed all the time and doubt I will ever use it.
@Jebiruph i have a question and that would be I have looked at t(e research you have done and as curious if the ESS battery does could one just run with the jumper installed all the time with the ESS negative disconnected, this would be having ESS disabled by what ever method one chooses