Problems with iPhone in iTunes managing music

I have a 6 plus and I am having trouble managing everything in iTunes. To start anytime I add new music it says copying music and it's always music I already have on my iPhone. For example the other day I tried to add like 30 songs and it added those but then it says coping like 1000 songs. I have a large music library but every song it was copying was already on my iPhone. So I have no idea where or what it was doing. I am also getting the famous explanation mark on some songs on my iPhone in iTunes. I know in researching this this problem would be making sure the song is still on the computer. The problem with this is I'm trying to work with songs on my iPhone so it shouldn't be trying to look on my computer for anything. There was also another minor issue where all of my music album wallpaper was removed. This all recently started happening, it was working fine for the first few months I had this phone.