Regarding your two questions here...

1. I do believe the plan was for it to work w/ manually entered orders, since there's a setting to not process recurring fees in checkout. What I'm doing is adding a checkbox to the order update form on the view page that will let you add the recurring fees to the order. The box will only appear if none of the fees have been added, so for any given order you'll need to make sure you add all the recurring fee products and process them at once. This was simple to add in and a functional bug since it was missing. I'll be committing it shortly. Note: you must be in debug mode to manually process recurring fees b/c of the way CC data gets stored.
2. The original plan included indefinite billing, but I decided that was a bad idea. As such, the module no longer accommodates that... it just had some stale messages that I've updated. There were just too many unknowns, esp. regarding expiring credit cards, that I couldn't accommodate with the 1.0 version of the module. I'll try to make this explicit. Maybe this can work in the future.

Also, I'm tweaking the module just a little bit so that only the card number and expiration date will be encrypted and stored in normal CC processing mode. Debug mode will store what gets entered during checkout, but this will not be PCI compliant if it includes the card's CVV and therefore is not recommended for live use. I'm sure more can be done to customize what's stored in the future, but I'm trying to change the bare minimum so we can put out the 1.0 release.