This is important information that can help to understand your problem.
Understanding the main idea I still don’t understand why you really have 4 pads for battery.
There should be no problem with connecting the same battery at one or at second side using these square and round pads. I don’t know what for are these oval pads. Do you assume other kind of battery. If so then instead of using the same pads for connecting battery on one and second side and crossing wires with jumpers I would consider using separate oval pads for connecting battery at one side and at second side and make right connections with no jumpers.