Syncing to iTunes after an iCloud restore and saving apps and folders

Here's my problem.

I used to not sync apps with iTunes. I can't remember why and have actually only just noticed this, but app sync was not enabled. I used iCloud to backup my phone automatically on a nightly basis, and have automatic downloads enabled on iTunes so although it isn't syncing apps, it does have copies of all my latest apps already downloaded.

Today I restored my phone from an iCloud backup. It restored all my apps and folders just as I expected. Great.

Now, I plugged the phone into my Mac to do an 'offline' sync and backup for good measure, which is where I realised iTunes is not set to be syncing my apps.

If I enable app syncing, iTunes starts from scratch, with no apps checked and if I pressed sync it would wipe all apps from the phone. I have many more apps on my iTunes than I have installed on the phone, so I can't just 'select all'. I'd have to go through the list and tick all the apps I have on my phone. This doesn't address the folder layout though, which would be lost.

I'm also not sure if, despite losing the app folder location, iTunes would still retain the app's data, or would that be wiped too?

I don't know why iTunes doesn't just use the phone as the 'master' and absorb all changes rather than overwriting. Very annoying.

Anyone know of a way round this? How can I sync my apps and folder layout back to iTunes?