in TO3000 you could create various jobs, with different payment terms and conditions and then add all these jobs to one invoice.
But I am not sure if this would be a solution for your problem.
I would like the create a invoice with some files. My problem is some of then I need to count lines and some others hours, by some other I will add a urgent extra charge. It is possible to "count" with differents definitions? I tried but do not find a way to change the count report. And if Practicount can not do it, there is other tool that can do that?