I mean you have to get in line and wait with other people. When you go to that place I mentioned, there will be a staff guy with tickets and with a jacket from the JE shop and he will ask you if you want to go into the shop, if you say yes, he will give you that ticket.
Though, my report is from 2007, I've been to the JE shop in 2008 and the shop as changed drastically. Also I've been there in November 2009 but didn't go to the JE shop in Harajuku, although I walked passed it, and girls were giving their tickets directly at the entrance of the shop and there was nobody at the place to stay I mentionned, so the system might have changed again.
Anyway, the shop is still at the same place as ever, so as long as you go there early, some staff will give you directions on what to do.