How is the best way to sync my iphone after a hard drive upgrade?

With a new hard drive on a Windows 7 machine and transferring my purchases (Mostly Apps, Music, and Photos) from my iphone to a fresh and the latest install of iTunes, how do i sync my apps the same way including the folders they are in on the iphone? Or do i have to drag them back inside their folders in the itunes software first? Especially, since it wants to delete everything from the phone and put the apps back on in that order instead of the folders I originally had them in...??

Try this way:
Disable autosync in iTunes, connect your phone to your new computer and right click on it in the device list and choose backup. iTunes will backup your phone without syncing.
Transfer your purchases the same way, choosing "transfer purchases" this time.
When you connect your phone for the first time, all media content will be erased. But you can restore your settings and app data from your manual backup afterwards.
Don't forget to set up at least one contact and event on your new computer to be able to merge calendars and contacts when you sync the phone for the first time.
About backups and what's saved:http://support.apple.com/kb/HT1766
How to back up and restore:http://support.apple.com/kb/HT1414
How to download apps for free again:http://support.apple.com/kb/HT2519
Saving other data is also described here. How

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