there is an option in JAM to pass up to 5 different values. The values to pass in the tpl_footer.php file are:
jrox_svalue_1
jrox_svalue_2
jrox_svalue_3
jrox_svalue_4
jrox_svalue_5
You can assign the zencart variables to any of these variables like so:
echo "<script language=\"JavaScript\" type=\"text/javascript\" src=\"http://www.domain.com/affiliates/sale.php?amount=".$TotalAmount."&trans_id=".$TransID."
&jrox_svalue_1=ZENCART_VALUE
&jrox_svalue_2=ZENCART_VALUE
&jrox_svalue_3=ZENCART_VALUE
&jrox_svalue_4=ZENCART_VALUE
&jrox_svalue_5=ZENCART_VALUE></script>";
Where ZENCART_VALUE are the zen variables you want to pass to store in JAM for that commission.
I'm not sure which variables you will be using, so you'll have to get that yourself.