Stall doesn't mean complete loss of lift, as even the turbulent flow will have some reduction in pressure, but usually means a large reduction in lift and large increase in drag. If you plot coefficient of lift versus angle of attack, as angle of attack increases, so does lift, but at soma critical angle of attack further increases in angle of attack result in reduced lift and this is considered stall condition. Usually this is aggravated by the fast than when lift is reduced, the aircraft or that wing will descend, increasing angle of attack, reducing lift further, possibly resulting in a snap roll.
When the flow separates enough to result in a stalled condition, the area under the detached flow is filled with vortices (as opposed to some gigantic stagnant separation bubble). I'm not sure what happens to the boundary layer, since the flow near the wing maybe just reversed (it's moving forwards at the suface of the wing).
Youtube video of real aircraft wing with streamers. Stall region first occurs at 55 seconds into video, with the streamers moving forwards (due to the vortice). The wing has washout (less angle of attack at the tips), so the root reaches stall condition first.
http://www.youtube.com/watch?v=bIsWseMbDQU&hd=1
In these video, although the flow is claimed to remain attached in some of them, it's actually seperating somwhat, but not enough to be "stalled". It's not clear how much of those small voids of separation are filled with a boundary layer or smalll vortices. These are relatively slow speed wind tunnels, so the stall regime occurs at very large angles of attack. For real aircraft, stall regime usually occurs between 8 to 22 degrees angle of attack, depending on the aircraft (delta wing's swept back leading edge can take advantage of small leading edge vortices, so they can reach 20 degrees or so angle of attack without stall).
http://www.youtube.com/watch?v=xW63SZ1LAqo&hd=1
higher speed lower angle of attack stall regime: