Syncing Apps from iPhone to iTunes and back

I've transferred my apps from the iPhone to iTunes by clicking on "Transfer Purchases" That's all good so now they both have the same apps.
I've installed the latest ver of iTunes so ultimately it allows us to re-arrange the pages of apps on the iPhone through iTunes.
When the checkbox "Sync Applications" is unchecked I can see my apps as arranged on the iPhone, when I check it everything is different. That's not what I want as it tells me my settings will be copied from iTunes to iPhone.
What I want is for it to recognise my latest apps setup on my iPhone and THEN allow me to re-arrange it from iTunes before syncing.
How can I do this?
Extra info: This is for my MBP, I've synced it with my PC and I think that has the latest settings I'm not too sure.
Message was edited by: mudbucket

As already mentioned, you can only sync to one computer at a time. To be able to go back to your computer, disable autosync in itunes, connect your phone and right click on it in the device list and choose Backup. Transfer your purchases the same way after that. Then sync your phone. All media content will be erased during this process, but you can restore your phone from the manual backup you made before. See also: "About backups": http://support.apple.com/kb/HT1766 and "Restoring" : http://support.apple.com/kb/HT1414

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