So I just got the iPhone 7 and synced my music and some music isn't syncing, also all of my downloaded music from Apple Music isn't on my music app.

What should I do?

Update iCloud Music Library on your computer, and then turn it on on your iPhone and choose "Replace"
If you turn on automatic downloads for the Music app, all of the songs will download. If not, then they will show up, but will be in the Cloud. I recommend turning on WiFi if you don't have unlimited data.

It's what I had to do when I went from the 6s Plus to the 7 Plus a month ago.

I see the option for iCloud Music Library on my Music settings on my phone, but have no idea how to do that on iTunes on my computer.

I have automatic downloads turned on as well.

Settings > Music > iCloud Music Library ticked on?

yes

Do you have a Mac or a PC?

It's under Library -> Update iCloud Music Library.

Mac. Pressed it and nothing happened

I used to have over 25GB of music on my 6 Plus and now only 2 GB on my 7

I hope you get it sorted out.