Dear Ken,
with small manual operation, it is possible to re-use the existing "sub-domain" website to make them available in JMS.
The key element is to install in the master website all the extension that are used by your existing domains as explained in the documentation, all the slave sites share the files and folders on the disk. This means that the extensions must be firstly installed on the master website.
When you have a master website with all the extension installed, you can create a slave site into JMS and rather than to use the Joomla install to create the DB and create the configuratoin.php file, you can copy your existing configuration.php of the sub-domain that you want to move into the deploy directory of the new slave site.
As your provide the configuration.php file, this will avoid that JMS request a new Joomla installation and it will use this one.
You probably have to modify this configuration.php files to change the path to the tmp and log directory. This may be performed using the Global Configuration of the slave site.
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