Yes you can have separated VM in each website.
This depends on the VM version.
With VM 1.1.x, to have separated payment, you need our additional extension to make the payment method configuration specific for each slave site.
There is also a limitation concerning the shipment configuration.
With VM 2.0, it seems that those limitations are solved because the configuration are saved in the DB and no more in files on the disk.
Concerning the VM templates directory, it will be shared.
So all the VM templates are potentially available in all the websites.
In terms of product and catalog, ... they are independent as such information is store in the DB and that each slave site have their own DB or at least different table prefix.
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