I've designed dozens of cars with Lionel, MTH, Weaver, Atlas, RMT, Williams by Bachmann, and USA Trains; in O Gauge, S Gauge, Standard Gauge, and G Gauge. Of all the information in this thread, the info from Jonathan (GG1 4877) is the most accurate; and there's even some new info in addition to what he stated.
Not to be a smarty pants, but the rule is, there are no rules. General guidelines yes, but there's dozens of variables in play at any one time which provide for more flexibility at times and more restrictions at other times from the manufacturer.
My professional opinion is to figure out EXACTLY what you think you want, i.e., what car, with what graphics, from which manufacturer, with which features (such as die-cast trucks or plastic trucks), and when you want it. Then go to that manufacturer and have the conversation about making it happen. Just be prepared to be flexible. You will likely have to make some accommodations to get your high priority desires while giving up on your low ones (for example, tight schedule could lead to higher cost; let go of the schedule to tack your order onto a the manufacturers next order and possibly cost savings. The same could be said for quantity sometimes; stand alone projects might have higher minimums than a project tacked on to a similar production).
Yes, each manufacturer has their own Point of Contract for custom run projects.
Feel free to reach out to me if you have specific questions to get specific answers.