Okay, I'm working on a scooter for my nephew that originally came with (2) 12 volt 12Ah batteries minus the charger. and I know I need to replace them with (2) batteries of the same 12 volts and lets

The Charger has to have 3 "Special" functions that an "ordinary" Car Battery Charger does not have.
A) OVER-Charging Protection : This is so you do not over charge the cells, and cause the hydrogen to release from the acid..... This could cause an explosion and battery acid all over the place if the case cracked and the contents of the cells leaked onto the floor.

B) Charge Monitoring - As the cell voltages go up, the current going into the battery slows down so that the amount of charge being put into the battery is equal to the losses from the battery on its own (Trickle Charge). When the Battery is in a discharged state the overall voltage may be 10 volts. (it should be only discharged to 85-90 % once in 20 cycles (deep discharge), the rest of the time it should only be discharged 75%.

So you tell me the Capacity of the batteries are 12 Ah. Lets assume you use up 75% of the 12 AH, this suggests that 9 ampere hours have been used up. To replenish that energy you need to put back in 9 ampere hours, plus 10-15% for losses in translation.
For a 24v system , this means that the Amount of current has to be limited to 2-4 amps at 28 volts. The Batteries need to be hooked up for 2-3 hours only, then checked for their cell voltage. once the cell voltage is at 1.25 volts per cell (check with the Battery manufacturer for confirmation) you can stop charging the batteries. they will be full

C) Over Current and Cell matching - The Charger has to be designed to pump out only so much current that the battery can handle (the Charge Rate). Typically for GEL-type cells, the Charge rate is 0.5 (this is 1/2 of the 9AH rating,) so the MAX that can be pumped in is 4.5 amps. Check with the Battery manufacturer to be sure. (see above about hydrogen)

Once you get the specifications for the battery(s) you can get the correct charger to match.

Not exact, to charge apropiate needs 10% more than nominal voltage. if not, will not charge the batteries.
And the charger its very important because you can over charge the battery.An example,if you have a 12 Amps Batteries each one if you put it in series will be 24 Volts.at parallel conection will be 12 volts but the double of Amps.
At serial connection will be 12 Volts the amps will be the same but the volts will be 24.

The charger at 12 Volts must be 13.8-14.5 DC Volts and divide the Amps in Hours.
The charger at 24 Volts must be 26-28 Volts. to charge well.

The charger for 12 amps batt example must charge 2 amps per hour at 6 hours = 12 Amps.(2 Amps Charger by 6 Hours Charging= 12 Amps.(Fully Charged.
3 Amperes Charger needs 4 Hours to charge 12 amps Batt.
5 Amperes Charger needs 2 Hours charging an a quarter
All of this is at DC Current.

Luck.