apps/ringtones in iTunes 12.7

hi, I download all my apps, app updates, ringtones iBooks etc on my iMac then sync to my iPhone/iPad, what am I to do now? I've read all the supporting documents etc. what happens when its comes to backup and restore to a new iPhone etc is all the apps etc going to be there? do I delete the Tones and Mobile Applications folders from finder in iTunes Media folder as iTunes can't see them now?

thanks in advance