You can connect either side, rectifier +VDC output side to Battery positive, or Battery negative to Rectifier -VDC output side. Current meter will always be in series with the circuit that you want to measure the current. Before doing that you must make sure that your multimeter have the high current capability, or you will end up with a burned meter, since battery (specially discharge batteries) can get all the current that your generator can give, which may be much higher that your meter current carrying capability. I will send you schematics of the circuit, including simple series pass charging regulator.