HTML Help does not have a "keep window on top" setting:

Note that there is no Keep window on top setting for HTML Help. This property cannot be set in the help itself in HTML Help, it must be activated by the programmer in the call from the application program that opens the help. See the Microsoft documentation of the HTML Help API for details on how to do this.

HTML Help Options tab settings:

Allow secondary HTML Help windows:

If this is selected your secondary (user-defined) help window types will be displayed in external windows in HTML Help. Note that this is a global option: If it is selected all topics associated with user-defined help window types will be displayed in external windows (even topics in the TOC), and only topics associated with the Main window type will be displayed in the main help viewer.

If this option is not selected all the settings here are disabled for user-defined help window type definitions. Then these secondary windows will only define the background colors of the associated topics and whether or not they have a header.

Save user-defined positions after first use:

This option is only available for the Main help window type definition. If it is activated the HTML Help viewer will save the user-defined help window size and position in the registry and use these values the next time the help is opened.

Leave this option activated unless you have a very good reason not to use it. Most users hate it when programs reset windows that they have resized!

Visible buttons:

These options are used to choose which control buttons are displayed in the help viewer. You may want to switch them all off for external windows.

Window has a navigation panel:

This option activates or deactivates display of the help viewer's navigation panel containing the Table of Contents, keyword index and other tabs. You may want to disable this for external windows. Note that if you also disable the Hide/Show button (see above) the user will not be able to activate the navigation panel at all!

Search tab:

Favorites tab:

These options activate or deactivate the display of the Search and Favorites tabs in the navigation panel. Note that if they are disabled it will not be possible for the user to enable them.

User-defined buttons:

Allows you to define two HTML links (i.e. URLs) as targets for the Home button and two user-defined buttons. (These buttons must also be activated in Visible buttons: to be displayed.)

You cannot enter links to topics in the help here. Note that you must enter fully-qualified URLs including the protocol (i.e. http://, ftp:// etc). Simple URLs without the protocol (e.g. www.domainname.com) will  not work on most users' machines.

You can edit the names of the Jump 1 and Jump 2 buttons but you cannot change the name of the Home button.