Adding music to iPod touch and deletes second later!

I'm having a really frustrating time with my 64 gb iPod touch. I'm dealing with the infamous exclamation point and disappearing of songs. I've noticed that this happened since the upgrade to ios 7 and itunes 11. It completely took out my 3,000 song library that was ON my ipod not on my itunes. I have been using a very simple technique since the early dawn of iPod and itunes which is I download a song, load the song to my iPod directly and not itunes and then delete the song. I've noticed that I can't to this anymore and it's really frustrating :/ I still get the exclamation points to songs that I have saved to my computer (not on itunes tho) do I really need to have my music that's saved on my computer to itunes? Is that the only way for itunes to recognize the music on my iPod ? I've been really frustrated and I honestly don't know what to do anymore. Is there anyone that can help with this? Is there another program other than itunes out there compatible with iPod?