Maybe a description of the area will help.
There is a big plaza shaped like a square.
Disneyland's entrance is the top of the square, California Adventure's entrance is the bottom and the security checkpoints are on the sides of the square. The ticket booths are inside the square and so are the actual lines to the park entry turnstiles. (T is the Ticket Sales booth and SEC is the security tents.)
----------- DL ---------------
l_______turnstiles___________l
l _________________________l
S____T______________T____S
e________________________e
c____T______________T____c
l _________________________l
l_______turnstiles___________l
--------------DCA------------
As Bumbershoot said - don't go straight to the turnstiles if you get there too early and security isn't there. Stop where I marked "Sec" on the drawing and wait in line there. It's a non-issue, if you arrive after the security personnel - you have to filter through the security area before you even access the plaza.
Best news is that once you do the security check in that spot, it's done for both parks - as long as you don't leave the Plaza. If you go out to DTD or your hotel and come back, you simply have to pass through it again.