Andrew,

I think all the problems your having are because of your order pane setup. I'm going to try improving documentation on this. You definitely need to remove the Payment panel and the Bill to panel for your order entry screen. Try double-checking this (from the updated documentation):

5) Order panes (admin/store/settings/order/edit/panes):
-Disable the Payment pane and enable the Credit Card Payment pane for all screens.
-Disable the Bill To pane for the Edit Screen. (You may leave it enabled for
view, invoice, and customer, but it will only contain address data when a
new credit card has been entered)

I'm going to update v0.4 with the doc change and a small improvement to new credit card validation on the order screen, so you also might want to grab that.