This answer describes how to enable specific features of Interlinks Manager with custom post types.
Generate automatic internal links on specific post types
The post types where an automatic internal link is applied are defined with the Post Types field associated with the automatic internal link in the Interlinks -> AIL.
You can also set the default value of this field with the Post Types option available in the AIL tab of the plugin options.
Analyze specific custom post types
The post types considered in the analysis performed in the Dashboard and Juice menu should be defined with the Dashboard Post Types and Juice Post Types options available in the Analysis tab of the plugin options.
Generate internal links suggestions from specific custom post types
The post types where the algorithm used to retrieve the internal links suggestions looks for suggestions should be defined with the Source Post Types option available in the Suggestions tab of the plugin options.