Syncing my iPhone with a new MacBook Air?

I've just bought a macbook air and have started syncing my iPhone to my iTunes account. I logged into my iTunes like normal but the only songs that were there were the ones purchased recently via iTunes. I usually buy my songs from a different source and put them on iTunes manually. If I sync my iPhone to iTunes will I lose all of that music or will it be transferred to the iTunes account?

You didn't make it clear what you need to do. The normal process is to buy music and download it on the computer, because of course, the cost of Internet downloading on a phone is much higher. Then the sync process is FROM COMPUTER TO IPHONE. If you want to do a reverse "sync" (from iPhone to computer), use iExplorer: http://www.macroplant.com/iexplorer/ (iExplorer, free, for OS 10.6 or later)

The other way you might end up with music on a phone that isn't on your computer is if the iPhone was synced to a second computer, and of course, Apple can't possibly support using an iPhone to "gather" music from many computers.

If the songs are purchased from your Apple account, you can transfer the purchase music to your iTunes. If you purchase your music from other store other than Apple Store, you can't do that.
You have to first transfer your music from iPhone to your iTunes and then sycn your iPhone with your iPhone with your iTunes. To transfer your music from your iPhone to your iTunes, you can use Fonetrans for help.

It depends if you used a legit apple supported way to purchase or if you just put audio files you downloaded on your phone. You should probably back up your iphone onto your old computer and then try and if it deletes them just download the backup onto your phone and try something else