Most of you guys won't like my method; it's just how I do it. I don't use the priming system at all. I size and decap the brass, wet tumble, then prime using an RCBS hand priming tool.
I'm pretty new to the 550 myself. I haven't even thought of the question re. how to empty the primer tube magazine. I've loaded both rifle and pistol cartridges on the 550 and find I can go the whole distance loading pistol. But not rifle. I've loaded .223 and .308 on the 550; nobody has been able to explain to me how to trim rifle cases on the device. Or remove sizing lube between station 1 and 2 (said mostly tongue-in-cheek). So far, I've been sizing brass on a single stage press and then trimming. I've been priming using the Lee Auto Prime Bench tool, which is pretty fast and can be done at a table sitting down. I could prime my sized .223 brass on the 550; but I've been leaving my small pistol primers in the magazine and it's just easy to leave them there for the next pistol session.