If you have both a private server (either iTDS or CTAS - you can follow how to set these up and configure them on the server setup page) as well as the Paterva server you will have certain transforms that are duplicated between your local server as well as the Paterva servers on the Internet. This gives you the option to run transforms against any of the servers you have configured. You can also disable a particular server or 'load balance' between two or more servers.
Load Balancing / Selecting Servers
When multiple servers are configured within Maltego and transforms have the same name you will notice that within the context menu has an extra step as seen below:
By selecting the particular server (in the above example "CommercialTAS31" or "Standalone CTAS") you will then specifically tell the transform to run on that server. If you however selected "All Transforms" in the above screen shot it would randomly select where each transform would run from the available servers.
Disabling / Enabling Servers
Within the Maltego interface after configuring the various seeds you have the ability to enable and disable servers. To manage the servers click on the "Manage Transforms" button under the Manage tab and then select the "Transform Servers" tab at the top, as seen below:
Once you are on this screen you can enable and disable servers via the checkboxes: