New iPhone - Enabling Sync Apps Help after having an old iPod Touch that was overloaded

I had an iPod Touch and it was overloaded with apps. So when I got the new iPhone I decided to start fresh and didn't sync it with iTunes immediately. I have about 50 apps on my iPhone that I actually want, and there are atleast 200 others on my iTunes that I don't want or need.  When I plug in my iPhone and go to the apps tab on my iPhone, the sync apps isn't checked.  If I check it it deletes all my apps on the preview window on the right, and none of the apps are checked.  So I deleted all the apps on my computer and transfered purchases so i only had the ones that are on my iPhone.  Now when I check sync apps, if i check all the apps, they are not in the right spots.  I can move them later, but my real concern is whether or not it will delete anything I have done in the app like game progress.  Any help would be great.  Thanks

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