You're right, I feel like Jon Snow, I know nothing!
I just tried it again and it has all the apps I have on my phone selected with where they are on my home screens. I can just drag the individual app I've downloaded onto my home screen and click apply.
Before when I tried it, I had loads of apps I'd previously removed all selected and on my home screen in random orders. I think it may have something to do with automatically syncing when the iPhone is tethered and/or transferring purchases, but I'm not sure.
I didn't mean to be rude to you (Allan Sampson ... lol) with my last comment, but re-reading that message it does sound a bit rude. I was just trying to put across the problem I was having and ask again if a single app could be synced without affecting the other apps.
It's worked for me now though so thanks for your help.