entering data into check registry to brakedown by customers

With a new small business with 4 or 5 customers how do we entering data into check registry to breakdown by customers? Customers need to be billed for hours and they also pay for services that we purchase for them and make a commission on. We need to have invoices generated by customers for hours of work and purchases for them. We have entered customer business but do not know to breakdown income and expenditures by customers. Do we need to set up separate categories on check registry? We have one copy of Quicken but 2 sets of files one business one personal when a entry of income or expenditures the memorized pop up category ( first box second line) comes up with previously entries the both personal and business files but does not show how to assign to a customers account. Is this where to make the assignment to customers or am I missing something? Any guidance would be greatly appreciated. Tim