Yes, you can. Vm2Mage does not require a clean Magento install. All products, categories and customers that are migrated from VirtueMart, will just be added as new entities to MagentoTM.
No, the migration using Vm2Mage is taking place over HTTP, which means that MagentoTM and Joomla!TM can be installed on separate domains and even separate webservers. This puts down the requirement that firewalls need to allow incoming and outgoing HTTP-traffic and that domainnames can be resolved properly on both environments.
