Syncing apps and deleting apps that aren't on home screen

My first question is about syncing apps. Should apps that I install directly on the iPhone from the App Store (not through iTunes) not show up in my synced apps list? At first syncing apps gave an error (I forget what it was) now the last time (or time before) that I synced it asked me to register the computer for syncing apps (or something like that) so I did. There are only a few apps showing in my apps section in iTunes (ones I tried downloading and syncing to my iPhone but unsuccessfully so I used the App Store on my iPhone to install them). At least I was smart enough to test it with free apps. So, I'm wondering if my apps don't show on the apps page (in iTunes) and I delete from my iPhone, that would mean that I wouldn't be able to reinstall without redownloading (and possibly paying again if it's a paid app), right? Is there a way to get my iTunes to sync my apps properly? Maybe its a Windows 7 problem?
Next question ...
I've downloaded more apps than fit on my homescreen but now would like to delete at least one of those. Is there a way to do this? This may relate to my previous question in that it seems to not be working to sync my apps so I can't use iTunes to control them. I will need to do it from my iPhone.
Another quesion relating to my first ...
If my apps are not synced properly and my iPhone crashes will I lose all my apps or are they backed up when the iPhone is backed up and can be restored from the backup?

They should. You can use File menu > Transfer Purchased From to move them, if needed.
Extra 'screens' show up in iTunes, on the Applications tab, if your software is the latest version. You can manage the apps there.
App data is backed up and can be restored. The apps themselves are synced, but not backed up. However, you can redownload apps for free:
http://support.apple.com/kb/HT2519

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