How do i get all my songs from ITunes to transfer to iPhone 5? They used to be on IPhone 5 but are no longer on there.

I have many songs that are listed on iTunes that are not transferring to iPhone 5 when syncing is completed. The songs have the checkmark so should be synciing. I also have many songs I do not want on my iPhone, they are not listed on my iTunes, and they won't delete off of my iPhone. I am so confused with the autofill, manual select, and this cloud business. Can anyone help me understand and solve this dilemna? I have the last update to iOS.