Checking the charging system
First the alternator-This can be checked easiest with the use of a 12V headlamp bulb.
Fit a pair of wires and clips to it. Disconnect the alternator wiring from the bike wiring. With the wires easily accessible, start the engine. Connect the bulb across any two wires; (using all three if you have them) the bulb should light each time.
If the alternator is a 3 phase unit the light will be equal across all three options. If the alternator is a 6V RM19 there will be a difference between the windings but as long as you use all 3 wires to obtain an output the alternator is in good order.
Final alternator check is to connect the bulb between any alternator wire and the machine earth. The bulb should NOT light. If the above tests prove good then there are no issues with the alternator. If alternator is good and A reg is good then the battery must charge. Provided the in-between wiring is in order.
Ammeters are not to be relied to prove that you are charging the battery. Measuring the battery voltage is the real proof. 12V battery should rise up to 14.4 V (ish) 6V to 7.2V a bit less with the lights on.. But the voltage must rise above the battery at rest voltage.
Cheap digital meters tend to pick up ignition interference, hence give erroneous readings. A traditional analogue (moving needle) or quality digital meter should be used. If you have a rising voltage but no charge on the Ammeter then there is a good chance (following any wiring work) the ammeter is wrongly wired.