Hi Manny, welcome to the boards.... you'll find MC to be a great app to use, and these boards a great community.
I think your first step is to figure out why Itunes is not seeing the Ipod at all. If that's the case then you might have a defective Ipod, bad USB port etc. I figure if Itunes it's the Native program that the Ipod is supposed to see then that needs to be solved first.
Right now using MC is touch and go for the new IPod classic as all features are fully implemented however MC is far far superior to Itunes and I would continue to experiment with MC.
You'll find that MC is lighting fast, very robust and can perform 1001 tasks that Itunes does not.
One word of caution is don't use both Itunes and MC at the same time to manage an Ipod.
By the way you may also want to disable the Ituneshelper or Ipod service on your windows Pc as that runs in the background and can slow down your pc.
Good luck and don't hesitate to ask more questions on these forums.