First the installation of JMS should only be performed on the master website.
The slave site should not have the JMS installed.
Second if you want to share the users, see the tutorial video 16
www.jms2win.com/tutorial#jms12x-16
Reveiw the concept of JMS that is presented in the tutorial video 0
www.jms2win.com/tutorial#jms12x-0
The fact that you say that you have installed JMS twice let me suppose that you have installed it on two separated joomla.
If this is the case, you have created two masters that are totally independent and where you will not be able to share anything.
The concept of JMS is to have a single joomla installation and all the other websites are slaves of the master.