My recommendation: First, disconnect the iPhone from your computer. If you're going wireless, you kind of have to throw out the wire (loosely speaking).
Now open the App Store app (on the phone), log into your iTunes account, and download the apps directly.
When you look up an app you already own, it will show the cloud-with-down-arrow symbol. New apps, of course, will show the usual Buy or Get buttons.
Once the apps are on your iPhone, from now on they will be updated automatically, if you have that option turned on in Settings > iTunes & App Stores.
Basically, this process cuts iTunes on your computer out of the loop, unless you still use it for backup. (My advice is to cut the cord completely, back up to iCloud, and use the wire only for charging.)