This seems like a good idea, and requested by a user:
We could have a Custom button in the Arrange Graphs Grouped form that would present users with a grid showing all graphs to be arranged with a Group field presenting a dropdown containing the numbers for the count of groups specified in the main form. Everything could start defaulted to 1 in the hope that this would at least be the right group for some of the runs. We would probably also want to implement "Fill Down (Ctrl+D)" for this grid, again to make it easier to assign a group to several runs at a time.
We could also, as I suggest in this thread, allow grouping by a replicate annotation, as we do for the graphs.
P.S. - Not higher priority than other work you are currently doing. Probably something for later.