My client has an existing non-JMS Joomla installation on www.clientdomain.com

Client then required a number of sites with the ability to pass information to each other so I suggested JMS.

I then set up master.clientdomain.com as the master and a slave on master.clientdomain.com/secondsite as a secondary site that would operate as a folder off the main site.

The client now wants the slave site built on master.clientdomain.com/secondsite to be the main site, i.e. www.clientdomain.com.

Should I now map www.clientdomain.com to master.clientdomain.com/secondsite?

I know that for an add-on domain, I would have to map the domain name to the folder in cPanel but how do I handle the JMS configuration if it's not an add-on domain but the main domain?

Thanks!

Yes, if you don't want to move the existing slave sites subdirectory into another place for the clientdomain you have to effectivelly map the domain to the location of the master.

Remark:
If the master.clientdomain.com is a public wesbite, search engine might also discover the subdirectory and give a ranking penalty in case of duplicate content.

So if "master.clientdomain.com" is private and not public, this is not a problem.
Otherwise, you should consider moving the subdirectory into another place for the www.clientdomain.com

See also our tutorial video 0.b slide 21-24 that give recommendation concerning the architecture and directory structure to ensure that subdomain and domain always have specific unique directory