My entire library is currently on iTunes because I have an iPod. I have consolidated it and all my songs are neatly in their folders by artist>album. The only info each song contains is artist, album, album cover, track number, and sometimes disc number.

After installing foobar and loading my entire library onto it, by highlighting all the artist folders and dragging them into foobar, everything worked great. But I started getting problems when I switched back to iTunes to play some songs. Certain songs got out of order and when I synched my ipod I had two of the same artists in my artists list on my ipod. My entire library became a mess.

How do I fix and properly use both iTunes and foobar without messing up my iTunes library?

It might help to enable compatiblity mode (extended preferences), as foobar writes ID3v4 tags and Itunes afaik doesn't support it. Note that custom tags will be lost on tag update. To get more info do a forum search.

Where is this compatiblity mode?

File-> Preferences -> Advanced -> Tagging -> MP3

if you were using foobar for ipod support, I would stick to that if you are comfortable with it (unless you really like foobar) -- check out foo_dop which provides the support for iPod's and works pretty well. Sticking to one player can also alleviate that problem although I dont know what the specifics of your situation are so I cannot give any further advice.