In EDC’s SDS buffer-system the SDS runs behind the Bromophenolblue (BPB). This means: Stopping the run with the BPB will left ~1.5 cm SDS in the separation gel.
Let the SDS run out of the gel and use the separation distance for your proteins by optimized shutdown:
a) You can see the backside of the SDS-zone:
mark it with Conchenille in the sample buffer.
Let it out in the anodal strip, then shutdown.
b) Use a prestained standard and run it till the 10 kDa stays just before the anodal strip.
See also 2D-trouble-shooting: “optimal shutdown”