Yes, what you describe will work. If you use the website to book your tickets, you're limited to four segments. You will receive a minimum of 100 pts for each segment, and you can give all the tickets to the conductor. Since this is still one reservation, you'll get all your tickets at once, whether you visit the Quik-Trak machine or have them mailed to you.

However, while this works for me on the unreserved Capitol Corridor trains in California (where there is generally only one "fare bucket"), breaking up an itinerary into separate segements may subject you to the highest "fare bucket" on other trains.