Interesting that your Doctor is putting you on Prednisone. Have they tried any of the immunomodulators or biologics? I was only on Prednisone once, during a hospital stay for a small bowel obstruction. The Doctors wanted me to taper off pretty soon afterwards and start Humira. As it turned out, I suffered a severe side effect to the Humira so they discontinued that and put me on MTX.
Regarding your question: My understanding is that Entocort is a topical steroid. It has a coating that doesn't dissolve until it is in the ileum of the small bowel (the most common site for crohn's). Once there, it's action is focused directly on the ileum and has little systemic action and hence fewer side effects. Prednisone by contrast, is systemic, effecting the whole body including the small bowel. So, I would not think there is any need to taper off Entocort before taking Prednisone