If I have graphs with different numbers of bars, how can I make the bars on all graphs the same size?

The key is to size the graphs proportionately. For example, a graph with 6 pairs of bars needs to be 1.5 times as wide as a graph with 4 pairs of bars. You can set the width of each graph in the General tab of the Format Axes dialog. In the case of a 6-pair (12 bar) graph and a 4-pair (8 bar) graph, make the 6-pair graph 6 inches wide and the 4-pair graph 4 inches wide.

Then, when you place the two graphs on a layout, from the Arrange menu, select to make the two equalize the size of the two graphs.

This command equalizes the scaling factor on the layout and the bars will come out the same size.