Re: do I then use CIM for purchases from my "members" and simply AIM to process individual transactions where I do not have a previously saved customer ID?
Correct. However, you should never use AIM for new development, use DPM instead. And likewise, you should never use standard CIM for new development, use "Hosted CIM" (see the api docs) instead.
You want to reduce your server's exposure to the card data (and to PCI) when-ever possible.
Re: why both AIM and CIM have a transaction processing method?
You're right, the Auth.net api's could be better integrated with each other. The good news is that the transaction fields for the different methods tend to be the same.
The feeling I get is that one thing they're working on is better integration between CIM, DPM and the ARB system. -- There should be no need to re-enter ARB payer info if it was recently entered as part of a transaction (AIM, DPM, etc) or is already within the CIM system.
I don't think Auth.net has many developers, so enhancements seem to roll out slowly. The good news is that their competitors are causing Auth.net to be more pro-active than they used to be. "All hail capitalism!"