Go to Add-Ins -> VBdocman menu or press VBdocman button on standard toolbar. Options dialog appears. Set Compile tab.

In the left frame specify which members (classes, forms, methods, events, ...) go to the compilation. Options serve as a filter here.
In the right frame there is a list of all available modules in current project. Check those which you want to compile. Unchecked module acts as if it would not exist in the VB project, so no topics for module nor for its functions, methods, etc. will be created.
There is also a check-box Add Help Context IDs. When checked, the context ID numbers are automatically generated and written into source code during compilation. Therefore if you are not sure, you should make backup copies of your source files before compilation. Help file of VB project is automatically set to generated documentation only if this option is checked.
The check-box Write to "Description" attribute specifies whether the description is automatically written into Description attribute during compilation. Description attribute is hidden in source code and cannot be seen in VB IDE. You can access it from menu Tools -> Procedure Attributes... or you can see it if you open VB source file in Notepad. Information in this attribute is compiled into resulting dll. So if you create your ActiveX control in this way and use it in other VB project, you can see that description in Properties window and in Object Browser as well. See also Creating and Using Context Sensitive Help.