Leaving the two batteries interconnected is fine for the battery tender.
You only need to disconnect either the positive or the ground from the rest of the motorhome to isolate the batteries; it's not necessary to do both. Generally, the ground is the one to disconnect/disconnect first so that any accidental short from the positive to the frame won't cause a short circuit and the associated headaches. (This is particularly the case when installing or removing batteries and working with wrenches etc. on the terminals. Disconnect the ground first and connect it last.)