Manual payment is not ideal for online selling as it adds a lot of overhead and also it is hard to glue other plugins together which are designed to work in an automated fashion. With that said, the manual payment option I have in place is not ideal but I am trying to improve it over time.
Using Affiliate plugin and eStore's Manual Checkout
Once a customer makes a payment using the "Manual Checkout" option the affiliate commission is automatically awarded to the appropriate affiliate at that moment. Why? Because it is a hassle for the shop admin to keep track of the affiliate ID of a particular sale (if applicable).
What happens if a sale do not go through? You simply reverse that commission for the sale. In the "Sales Menu" of the affiliate plugin, every commission that has been awarded to an affiliate has a "Buyer" associated with it (look at the buyer's email field). After you receive an order you will obviously track the money transfer from that buyer. If the sale do not go through then go to "Sales Menu" of the plugin and manually apply a negative commission to cancel the commission awarded earlier.
Why is this model better? Ideally, if a customer places an order then he/she is more likely to go through the sale so you will only have to cancel an affiliate commission on rare occurrences. This way you are not having to keep track of affiliates for every sale which should minimize your maintenance overhead a little bit.
Using eMember and eStore's Manual Checkout
The model I had in mind is that after a customer pays for a membership using the "Manual Checkout" you will manually create a member account from the "eMember dashboard" and let the customer know.
What username to use for the member as it can't be changed later? You can instruct the customer that he/she can enter the preferred username in the "Additional Comment" section when filling out the details on the "Manual Checkout" form.
The other option is to contact the customer to ask for his/her chosen username before creating the account. The manual payment transfer process will most likely involve a few email going back and forth between you and the customer. Somewhere in there you can ask for his/her chosen username.
