Syncing problems after iTunes created automatic playlist

Because I have more music in my library than can fit on my iPod Touch, iTunes created an automatic playlist that would serve as the folder for what would go on my iPod.
When this happened, only that playlist would sync with the iPod, so the applications I downloaded on my computer did not get synced onto the iPod, so I deleted the playlist.
Now, when I sync, nothing gets transferred onto the iPod.
How do I fix this problem? Also, how do I tell iTunes what particular songs I want on the iPod?

Click here and follow the instructions.
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