By default all Canned Comments are visible to all users with an E2CP license because the Canned Comment object organization sharing default is Public Read/Write. If you would like the limit visibility to Canned Comments, on a department by department basis, for example, you can change the organization default to Private and setup sharing rules based on criteria or ownership.
The New Comment page respects Sharing on the Canned Comments object. Organizations can implement sharing rules and change the Canned Comment object to an organization default of private.
For example, if you have multiple departments using E2CP and each department should only see canned comments related to their department, consider adding picklist values to the Category field on the Canned Comment object and using criteria-based sharing rules grant access to those records.
You can confirm that sharing is setup correctly in your Salesforce configuration by having users navigate the Canned Comments tab to check record visibility. Users will see the same records on the New Comment page that they can see in the standard Salesforce tab.
The configuration of sharing rules is standard Salesforce functionality and not supported under E2CP product support.
For more information on configuring sharing in Salesforce, see http://help.salesforce.com/HTViewHelpDoc?id=managing_the_sharing_model.htm