Is there a process for handling receipt of payments offline that allows for indicating which plans to approve? Or, is it an all or nothing situation?
All or nothing, that's why the user is asked to confirm. There is no "return rack" as you'd find in many department stores with CBSubs.
CBSubs is also not a merchandising platform, thus there is no "cart" to remove quantities, etc...
If this should occur, how can one handle it. Can a CBSubs admin cancel their current invoice and create a new one with just what they have paid for?
Delete the basket then edit the user via User Management and subscribe them to the plan they provided payment for.