1. RB1 should be the RB and RB2 should be the FB in Notre Dame Box. You can tell because the RB2 slot can be set to block. If you look at it that way, does it clear up the issue? Feedback on the default formation settings are also welcome. We did try to make RB1 the "rushing" RB and RB2 the FB in all formations just so in the case that you have the plain RB depth chart set to those two slots, it would pull your top RB in the rushing slot and the second RB in the FB slot.
2. The formation settings and the play settings tell you two different things. The distributions on the formation settings don't tell you anything about how the play is run, but rather just which players are most likely to be involved in the play based on how the play is run. The playbook play settings are what tell you how the play is run. For instance, you can say in the formation settings that you want a particular WR slot to get the majority of the deep passes, but you could set your playbook play to pass mostly deep or not pass deep at all. Another example would be that you set one RB to get the majority of the inside rushes and another RB to get the majority of the outside rushes. In your playbook play you can set the distribution of how many inside vs outside rushes you call for that play.