The Microsoft HTML Help format uses sets of definitions referred to as "help windows" to configure the help viewers used to display CHM files. Help window definitions can also be used to display individual topics in external windows when you link to them.
Help window definitions are only relevant for HTML Help output. Their settings are ignored in all other output formats.
In Help+Manual help window definitions are stored with your projects. Each project has its own set of help window definitions, which you can view, edit and add to in the Project Explorer in Configuration > Microsoft HTML Help > Help Windows.
By default there is only one help window called Main, which defines the configuration of the main help viewer for HTML Help.
You can define additional "secondary" help windows are used to display topics in external help viewer windows when you link to them. You do this by selecting the name of the secondary window in the Insert Hyperlink dialog, in the Window: field.
This is the only use for secondary windows, they have no other purpose and they are only relevant in HTML Help.