A 2nd Aux battery was optional on gas vans. This was used for both the trailer tow package, or to power the body-builder accessory circuits inside the van.
If you don't need it, Ford had a jumper wire which redirect the accessory circuits back to the starting battery. If you just leave things as-is, your accessory circuits will all be running through the aux battery charge relay, and eventually that will probably fail.
2000 E450 dually V10 wagon