1) Use a pack of needles for a project instead of just one. You can leave a snipped thread on a needle for when you need that color again. Saves a bit of time.
2) There were some DMC threads added a few years back that show up in my patterns on PCStitch, however they're hard / impossible to find now (3880s and 3890s). I've now deleted them from PCStitch so that it won't choose those colors first when uploading a picture, but find closer matches in available colors.
3) Print to PDF and then upload PDF to Pattern Keeper to track progress. So far it's been a lot easier to see what needs to be stitched vs. what has been stitched. I was afraid PCStitch wouldn't export to PDF, but the internet helped me figure it out. Phew.
Its often a bit of a challenge to find equivalent colours for some of the discontinued numbers.