When syncing apps from iPhone to computer which takes priority?

I spent time in iTunes arranging my apps. I then did an apply and the phone synced with the computer. What was on the phone replaced what was on the computer rather than the reverse. So all my re-arranging of my apps was lost. How do you control which one takes priority? Thanks!

I created a new user on my macbook and tried to authorize the computer but got the same authorization error. This doesn't have to do with the fact that I have once used a different iTunes account? (not since I have had the iPhone. I have tried to figure out how to delete this but it looks as if apple doesn't want me to.) Plus, it's the same email as my dot mac which I've ALSO been having trouble with the past few months-- it keeps resetting on its own and my keychain and iphone can't get into it. online chat has not solved the problem so i decided to just let it expire...
Ive been using a mac for 15 years and have never had as many problems as i've had these past few months.

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