Final Cut Pro X: more issues with synching

After adding a cross dissolve on to a single shot the beginning and end of the dissolve connects 3 shots together in a smoother transition. However, this editing technique appears to link all the shots together and it is now very difficult to move each shot independent of each other.

The shot below of our star singing into camera then became out of sync with the music track.
This was quite frustrating as we are aware that the synching process takes a long time. I had to move the clip above the the main time line of shots and then use markers to mark the point that Julian started to sing on the shot and the point in time where Ed Sheeran starts singing on the original track. This was made even more difficult due to the fact that we had already disabled the audio from the film clip. I eventually marked the point of singing and then proceeded to perfectly match up the two markers. Once completed, it was then a challenge to move the shot of  Julian into the main time line without disrupting other clips and the transitions.