The way you should work is to mark a sync point on all the clips in the Project panel not the Timeline panel. Then, once you have your sync points for all the clips you would make a multicamera sequence from that.
See Mark Clips for Synchronization: http://helpx.adobe.com/premiere-pro/using/editing-multi-camera-sequences1.html#id_78669
I understand about marking sync points in clips. Per the video you sent me to, the best way seems to be by setting the in point at the sync point for each clip in the source window.
1. Can't I then take the .mov and .mxf clips for each scene and place them in, say, sequence one on the time line and they will already be synced in track 1 and 2?
2. What sequence settings do I use ? The ones for the .mxf clips?
3.can't I continue by adding synced scene 2 etc clips into sequence 1?
4. can't I then create a new seq called "multi cam" and drag seq 1 into it and then do my multi cam editing there?
I find the best way to do this is to create one sequence and add all your clips to that. Sync them up manually.
Then create a second sequence, nest the first into it, right click and Enable Multicam.