As you changed the question to be more specific, I'll add a separate answer:
How do schools typically arrange the payments for course designs?
At the universities I have been associated with, a course is designed by the professor that teaches it, or as a collaboration between multiple faculty that are teaching separate sections. Many times you will find that intro courses that are taught by multiple faculty are still independently created -- a Calculus I course can be drastically different when taught by two different professors even if they are teaching it during the same semester. I would not recommend this, but it is frequently done this way. Savvy students will try to take the section with the professor who has the best reviews. Depending on the school, this is one forcing function for better teaching, although not a particularly good one.
To answer the question (Peter Shor's comment notwithstanding), course design is generally part of the duties associated with being a professor, and no extra payment or duty relief is garnered. I have never seen a case where payment is given for course design at the collegiate level. That is not to say that it isn't done, but I haven't seen it. I have, however, seen many cases where one professor will give all class notes, homework assignments, and tests to another professor in order to build his or her course from those materials, but this is done out of good will and not for payment.
Are course designs typically only made in a one-time payment, with intellectual property transferred to the university?
I have never heard of a royalty agreement for course design, and I would be very surprised if you could get such a deal. Universities do work out deals with textbook publishers for reduced rates on course materials if the book will be required for a class, but that is different from asking a particular professor/instructor to design a course.
Is it at all typical for course designers to ask to retain intellectual property rights and to receive continued fees for each semester that a course is used?
No. The bottom line is that courses are (read: should be) mutable entities that change with the times, and with the person teaching them. This is not to say that there shouldn't be a standard for a course, but I find it hard to believe that a college or university department would hand an instructor a set of materials and dictate that the course must be taught exactly in accordance with the set of lesson plans, with the same materials. I am all for providing helpful materials for instructors (as well as standards), but dictating them removes the creativity from the act of teaching, and limits the ability to prepare new material for the class.
To get off my soapbox: if you can design a course that your department will buy lock, stock, and barrel, and then you can convince them to pay you each time the course is used, go for it. You'll have to convince them that the course will indeed be viable next year and the year after, etc., but they may be willing to buy your argument. My suggestion is to work out the best deal you can for a one time payment, and move on.