I don't know much about the internal working of a battery, but I don't think you can tell exactly how much charge is left in them. On standard AA sized cells (the common 1.5V ones), there is a label on the side that says "1.5V, 0.5Ah", so you could time how long you have left from 0.5Ah, I suppose. The problem, as you know already, is that the multimeter can't "know" what kind of cell it is testing e.g. if it's a small 1.5V 0.5Ah cell or a large 1.5V 50Ah one. Also, I think that the current diminishes as the battery wears down, so a graph of time against current could help.