I have a Hitachi excavator that has two 24 V batteries that are hooked + to - which I think is series. How do I charge the batteries. Separate or together ?

Most things have a charger for their product.
2 12 volt batteries in series is 24 volts, A 24 volt charger would be easier than charging 1 battery at a time, or removing jumper from the plus to the minus, and charging both 12 volt batteries in parallel.

If this is 2 24 volt batteries in series, I would get a 48 Volt charger, or I would have to remove jumper and charge each battery separately or in parralell.
You can charge each Battery individually with jumper intact.