-48VDC battery bank?
Voltage is relative - it represents the work done by a charge to move from one point to another. If you're standing on the negative terminal of the battery, and you call the part you are standing on "ground", or 0V, the positive terminal will look positive relative to you. Standing on the positive terminal, you might call that terminal 0V, and then the other terminal would have a negative voltage.

Cutting a long story short, you can go ahead and design your battery charger as usual - with positive voltages - and just swap the wires going to the device consuming the power.

This works because what you consider to be the positive rail, the supply circuit will consider to be ground, and then what you consider to be ground will be negative with respect to that.