I have a couple of sites live, and a couple more in development (Iam doing dev on XAMPP on localhost currently).

If I implement JMS MS now, am I able to get these existing live and under construction sites to be integrated into JMS MS?

In speaking with a host we are very likely to use as our reseller account, he made the following statement (he dos say he isn't familiar with JMS MS so thought it wise to paste his comments and get your comment on it).

"Ok, what I was getting at with JMS is that it allows you to do what you said - develop multiple sites, with different domains, independent of each other (able to have different config settings, content, databases, etc.) but where I think the catch is is that they all have to be within the same hosting account.

For example in a reseller environment, your reseller account would be in a directory (on the server) as /home/your-account/. Then any clients who purchases an account from you would be on that same server, but their accounts would be in their own directory /home/customer1/ and /home/customer2/ etc.

From what I read I don't think JMS can deal with the different directories like that. I think it can only deal with the accounts being under your directory /home/your-account/customer1/ and /home/your-account/customer2/, etc. And reseller accounts don't operate this way - because of how the WHM / cPanel software is designed."

Is he correct in saying the individual sites need to be in the same folder structure or can we have www.site1.com, www.site2.com, etc?

NO this is not correct.
JMS is able to deploy slave site into /home/your-account/customer1/ and /home/your-account/customer2/,

The only issue you have to consider is the server permission.
Frequently when using different hosting account, the owner of the directory "customer1" and "customer2" are done in a such way that you can not have the permission to read/write into the other directory.

If you give the permission to write in the other directory, JMS will not have any problem.
We just mentioned that in general, the permission is not allowed when working with different account.

As long you provide the permission in the directory as long JMS will be able to deploy the symbolic link and access the files.

As you have WHM (and therefore a root access), you can always manager the directory permission to allow writing across accounts.