MarkT:
Yes, that's pretty much it - don't join the negatives of panel and battery unless the charge controller does.If they are not at the same potential you'll have to find out which is most negative, use that to common with Arduino ground, and measure the other one's voltage with another analog pin (and possibly divider).
Its fairly likely the negatives are common though.
Excellent. Thanks for the comments - especially about what to do if they are not at the same potential.