Thanks. I'll recheck all this.
With regard to the orders, I "found" them finally under Admin->Customers->Orders. I have been looking under Admin->Reports. Are there any more detailed reports or logs that I should be looking for or contributions that enhance the logging? Oh, related note: where do I change the graphics for the corner of the Invoice/packing slip? (from the default osCommerce). My site has the logo swapped already.
For the already paid item, this would seem to be the issue when you're using multiple stores, right? If I only have once store, appending a letter still isn't going to help. Or is this an issue with using the sandbox that needs to be adjusted? I had already tried setting Paypal to allow duplicate order numbers, but that didn't seem to impact the sandbox... I haven't tried to issue live test orders for a penny each, but I'll probably have to do that at least twice to make sure things are really working.
Sorry for all the questions. I've got the IT and web background, just very new with the store stuff (and all the baggage that goes along with it).