I have done a few, but not using CE Pro, but I imagine the process is similar. You need to sync them up by sliding the tracks back and forth to get them in line. Find a beat, like the kickdrum and line them up as best you can. Now zoom in closer and closer so they are right in alignment.
My clock and the one that phish uses for their releases were off almost a full second after about 50 minutes, so I had to split up the SBD source and resync every-so-often. Here is a picture from the session... Sorry it's so big....