scanner . try your local auto part store.preferably where you bought the parts.explain to them you replaced the alt. and batt. make sure that charge system isn't for your air conditioner..(quiet possible)
The OBDII system has nothing to do with your check charge system warning indicator.
The only thing that will light the indicator is a charging system that has insufficient amperage or voltage...or a wiring connector that has an issue.
Answers are correct, low battery voltage can cause drivability problems when voltage drops too low. Probably a bad alternator or wiring issue. Turn on the ignition switch to the on but not run position do you see an icon on the instrument panel representing a battery, if you do not see this battery icon the alternator is not seeing power to allow it to charge. Start the engine does the battery icon go out. Put a volt meter across the battery terminals with the engine off, at rest the battery voltage should be 12.6 volts if the battery is fully charged. Now get a friend to start the car while you watch the voltmeter, the voltage reading across the battery should read approximately 14.6 volts if the alternator is charging correctly. This is just a crude check of the charging system.