Dot 3 and 4 can be mixed, dot 4 has a higher boiling point. Avoiding having the master run dry is prefered, its just easier not to have to bleed air from the master, if it happens its not a big deal just takes longer. Also if the truck has ABS you don't want the ABS module to get air in it because that can be a real bitch to bleed, sometimes it even takes a scan tool, however if you keep the reseviour full of fluid you'll avoid any of these headaches.
Like Tom said above just do one line at a time, keep the master full inbetween. Then to flush the system just keep bleeding until you get clean fluid all around. There are lots of tools for flushing and bleeding brakes, all of them are just fancier ways of moving fluid through the system, having someone pump and hold while you open bleeders will work just fine.