Magento

I am not sure if I overlooked something, but I’m trying to configuring multiple shipping groups in the same way you would do a catalog price rule. My company does both wholesale and retail and some of my customers use their own shipping methods while some use my account with Fedex. Also I want to charge a handling fee for the customers I do drop shipping for while I do not want to charge a handling fee for a brick and mortar customer. I would like to configure these rules into the customer groups. Thank in advance for any suggestions!