Custom programming.

I don't know about generating the actual CM, or what part of the process is time consuming, but here is what I might do - depending on how variable the lists are (maybe you're already doing something similar and I'll apologize in advance if I've insulted your intelligence):
 
Set up each customer that gets commission as a Salesperson. You could ostensibly use an unused field on the SO (for instance, we never use Job Numbers), but by setting up salespeople you are forced to select a viable customer.
 
Then I'd use Crystal Reports to generate a report. The potentially tricky part is, as I implied, how complicated your list is. For instance, if your commission amounts could be defined by a fairly short list of Category, Class, or Part Numbers, or could be limited by using wildcards, it would be relatively easy using an if/then statement.  If each customer gets paid a different commission by part number and you've got 5,000 SKUs that would be a bit burdensome. If there are lots of PNs, and every customer gets the same commission by PN, I would try to find an unused field in the Inventory file that could define the commission amount.
 
Once you had the report set up, you'd just have to print it and enter a single CM for each customer. You could make the report so that each customer was on a separate page, and send it along with the CM.

Lenette,
 
This is truly where custom programming comes in.  You can try to figure out 12 different sorta work-arounds that with enough effort might give you a semblance of what you are after.
 
OR, you can commission a custom program that will ALWAYS do this and will prevent all but the most bizarre mistakes and give you convenience and flexability.
 
Now this could be done as an integrated item in TAS so it is literally a prt of your program, OR it could be done as a linked application (using ODBC) in something like MS Access (to keep the costs reasonable) where it would be tracked and reported separately.
 
Your choice - cheap and a pain, or some cost but it works.

Lenette,
 
Sent you a private message in regards to this.