As long as the two negative posts both go to a common ground, they do not need to be connected together as the ground will connect them.
Going back to your ORIGINAL post, you said that you smelled an electrical odor from the house battery area. Usually when there is an odor, something is usually fried and is no longer working as designed. I would look for whatever burned and start from there. Check all fuses even if they look good. You can also apply 12 volt power to your jack pump and see if it operates. You have a few different interlocks that must be in the correct position before your jacks will operate. It might be time to go back to your manual and make sure that you are trying to retract them according to the book.