My method is stuff that I have to keep dry (quilt, down jacket, synthetic pants, warm socks, any extra clothing) goes in the compactor bag. I twist the top and jam it down. Then I pack stuff that can get wet on top (bivy- this can go in either but I tend to leave it out, tarp, cook kit, rain jacket). This keeps everything that needs to never be wet, not wet. I have a pretty rain proof pack as well.
Edit: Oops, See above. He beat me to it.