Jump-starting a machine with dead batteries may keep a job running temporarily, but it's a quick fix with steep long-term costs. Alternators are not battery chargers. They'll push enough current back through a healthy battery to assist its natural recharging process, but an alternator is not powerful enough to bring dead batteries back to their normal state of charge. Unless you thoroughly slow-charge batteries that have been deeply discharged, each time you start the machine the batteries will degrade slightly. The answer: Get a battery charger out to a jump-started machine before it will need to start again, or swap out a fresh set of batteries and send the discharged set to the shop for proper charging.
Charge groups of batteries in parallel and set a constant-voltage charger slightly higher than the intended charge level. Charger amperage should never exceed 10 percent of the battery's rated amperage. Deeply discharged batteries should be charged more slowly. If a battery heats up, slow down by reducing charger voltage.