What kind of unit do you have?
It should be fine to leave your slides out and not have your jacks down.
I know nothing about the charging system of your unit. But if I was to guess (do you have a owners manual) I would say that the RV shore power cord will charge your house batts, but not your charge your engine batts at the same time... but your do state there is a manual disconnect switch???
State your unit and someone with the same type will give you a much better answer.
2013 Forest River Salem Hemisphere SBT312QBUD
2001 CrewCab F-250 7.3 PowerStroke Diesel
SuperChip, BTS transmission, 6.0 Trans Cooler