I signed up for Adsense w/ one of my sites. I then opened another, non-related site and put up adsense there, using my original Adsense account to generate the ad html. Is this how it's supposed to be done? How do I track which site is generating more clicks/money?

Finally, I've been reading on the boards about other programs like Chitika. Is it ok to have these ads AND adsense on the same site?

You can create separate channels in adsense for each of the sites/pages to track them individually.

I believe Chitika's TOS allows you to show it and adsense on the same page but you might want to check on that.

I created the channels ok but when I generate my ad code they aren't listed. Will they still display by channel in my reports? I tried doing a "custom channel" and that is listed under the "channels" option in code generation page...

Yes I saw on chitika that you can put them both on same page