Unless you have selected "Centralize Logging" each site in your network will have it's own log which means that your users will have a unique balance on each site.
If you on the other hand enable Centralized Logging, you will have all sites in your network logged into one central log and with that also centralize your users balances and history.
If you have already log entries in several sites and switch to centralize the log then all sites logs will be ignored and everything focused on your main sites log (blog id 1).
Basically your users balance is stored as a user meta in your usermeta table.
The default balance is stored under the meta key mycred_default or if it's a custom point type - the meta key you set yourself.
This means that you can technically get a users balance via the get_user_meta function that WordPress provides.
On multisites, all user meta on all sites are stored in the same usermeta table.
To make sure that your users can have a unique balance on multiple sites (if they are a member on multiple sites that is), myCRED appends the blogs id to the end of this meta key so it becomes:
When you enable "Centralized Logging" this appending of the blog id is removed resulting in the user having the same balance on all sites.
You do not need to have the "Master Template" enabled to use the "Centralized Log" feature as they both control two different aspects of the plugin.
I unfortunately never used the WP Multi Network plugin so it has not been tested with myCRED and I can not guarantee it will work as intended.