one cart driving two seperate websites...?

Hi Dominic,
  Please see : http://wiki.earlyimpact.com/productcart/licensing You must have one licence per live store.
In addition if you try and share a merchant account you will almost certainly run into difficulties because the response address is usually fixed to one domain.
An alternative is to feed two sites to a single store and separate the looks by passing a session variable via the link which can then be used to determine which header and footer to use. See : http://wiki.earlyimpact.com/how_to/show_different_content_customer_type
Of course the URL's would be the same for both "stores" (and the products), but the look can be varied. You also need to consider which one would be the default if customers arrive directly to the store pages. I'm not sure of the SEO implications of this from Google's point of view.

OR easiest of all, run two separate copies of ProductCart :-)

There are compromises and difficulties with both approaches. For example - stock levels if you run two separate sites. That may or may not be a major issue depending on your circumstances. The item duplication is straight forward though, using the export for reimport wizard, or just import data for both sites using a CSV or spreadsheet.