Completely messed up my iPhone syncing to iTunes!

Amateurishly, I have fiddled around with settings and ended up with chaos. I need some serious tidying up done.

I have an external hard drive; all of my music is on there. I have an iPod (which all my music sits on) and an iPhone 4 (which I regularly put my newest music on. I have a playlist for each of these to automatically sync to.

At some point, I changed the default iTunes media folder location to the music folder on my hard drive. This is when the trouble started.

My iPhone syncs photos, and music; but there are issues. Apps are no longer synced. I update my apps regularly on the iPhone itself, and download plenty of new ones, but iTunes thinks I am a good 40 or so updates behind. When I connect my iPhone to iTunes and go to iPhone settings on the iTunes sidebar, Apps is now no longer ticked to automatically sync? When I tick it, a prompt warns me that this will update the apps from my iTunes to my phone. I am worried this will remove everything I have done on my phone since the change?

Also, there seems to be another copy of the playlists (and perhaps library) elsewhere? I know this because some albums that used to be on an old playlist for my iPhone wont come off the phone, even though they don't show on the playlist on iTunes.

Also, whereas the hard drive used to be lightning fast, I am worried that an iTunes library has popped up somewhere else, as using iTunes now is extremely sluggish.

A final problem is that I can't seem to keep up to date with software updates because of these issues. I tried updating my iPhone through iTunes but a warning message came up. (I'll try again if you need more info.)

So what I need help with is!!
-backing up my iPhone
-making sure that everything on my iPhone is transferred to my iTunes library
-checking I have just one iTunes library (even if these means starting it again)
-whatever else you think of.

I apologise for my ignorance and look forward to anyone's help.