Syncing music from iTunes to iPhone.

it says that I gotta reset my iPhone to Factory Settings. Which means I will lose all my apps, contacts and stuff.
Why would you lose anything? Your contacts will be in whatever desktop program you have chosen to sync your contacts with, your Apps should be in your iTunes Library, and everything else should be on your computer too (assuming youve been syncing/backing up as designed).
Are you trying to sync music from a different computer than you normally use?
iMac 20", MacBook, Time Capsule, Airport Express, AppleTV 2 Mac OS X (10.6.6) iPhone 3GS 32GB, iPad WiFi 32GB

I install / buy apps from App store on my phone, I do not attach my iPhone to my Computer then install / buy apps there. But if I install my apps on my computer so I have them on iTunes library will they come along when I sync music to my iPhone? And well, I have these saves when I sync music and reset it asks if I want to go back to another save Ive done earlier. And I just see Music, Films, TV Shows, Podcasts and radio.
Alienware m15x Windows 7 No