Line Item commission maintenance

We have Several items that will only have 2.5% commission where the sales person has a commission rate if 9%,

sages docs are on clear on how the SO line item commission maintenance works and what effect it has on the sales person to customer relationship,

can someone please shed some light on this, currently we use a crystal report that uses the ar history tables to do the commission report

mas2014,  sp4

Thank you, Tj