I have multiple apple ids was backing up everything to iCloud from iPhone 5. I just bought iPhone 6 and perform a iCloud restore. I received a message that all files did not restore.   How can I restore apps, files manually?

I have multiple apple ids was backing up everything to iCloud from iPhone 5. I just bought iPhone 6 and perform a iCloud restore. I received a message that all files did not restore.   How can I restore apps, files manually?

Yes - I connected my phone to my computer / Itunes and went into the apps section, but from there I have no idea how to manage the push notifications.  I even tryied going into itunes that is installed on my phone.  I still cannot find anyplace to manage these popups.  I have also gone into settings - notifiations - and tried turning all notifications for these apps all off but that didnt work either.  Any guidance is MUCH appreciated - Im not sure where to go from here.

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