I mark my cut down Luger case heads with a sharpie. I haven't had any issues sorting out my brass yet....
Given the distance my P64 and CZ-82 like to throw brass, my recovery rate on my cases (has been as low as 50% and as high as 90% with extensive looking), and the availablility of once fired 9mm Luger brass (it is all over the range), I much prefer to cut down Luger brass to Mak specs than spend the 18 cents per case for backordered Starline.
I use the Lee case trimmer to cut my brass down. The only problem I have had is wear on the case trimmer pilot gauge tip. My cases were getting shorter and shorter until finally they were out of spec (after only 200 cases!). I noticed the tip of the case length gauge was starting to mushroom. I called Lee and the tech said "you must be using some power" (yes, cordless drill) and "once it bottoms out, you're done. Don't ride it!" (yeah, OK, I get it.) Lee did send me another one.