1993 Other Mitsubishi Models battery/altanator?

Ive recently purchased a 1993 mitsubishi RVR I ran the battery flat as I had a belt removed I put in a different battery and found it would start and drive but I could not operate my electric windows or heater I attempted to charge the original battery and put it back into the vechile this alowed me to operate windows and heater but when the original is in the car the battery light in the dash comes on? I tried a different battery the light did not come on but the car ran but stil unable to operate my windows or heater could this be and altanator issue or the original battery bein flat and that car only being able to use the original battery?