After spending a whole day installing a fresh copy of Mac OS X v10.8 (Mountain Lion), Xcode 5, fixing provisioning profiles, certificates, creating new ones,
Stupid as it may sound but all "Provisioning Profiles" re-appear under "Organizer - Devices" once you connect a real device.
For me, the refresh in xcode 5 prefs->accounts was doing nothing. At one point it showed me three profiles so I thought I was one refresh away, but after the next refresh it went back to just one profile, so I abandoned this method.
If anyone gets this far and is still struggling, here's what I did:
When I did this, everything synced up perfectly. It even told me what it was downloading each step of the way like good software does. After the sync completed, I closed xcode 4.6.2, re-opened xcode 5 and went to preferences->accounts and voila, all of my profiles are now available in xocde 5.
You can add account in the preference -> Accounts setting.
It seems that you already configure xCode4, then I think you can select your certificates for compiling in project-> Building Setting directly since your certificates are already in your keychain.