Compiling
To create a compiled help file, open Scrapbook and right-click on the desired entry in the sidebar. Select the new entry "Create CHM" to start the compilation.

You may see a command line window appear as the compiler runs. Once compilation is complete your file is ready. Scrapbook CHM Creator creates the file in the directory selected in the preferences dialogue. By default, you will also find the HTML Help project files in Scrapbook's data directory for the item you selected in case you want to make changes manually.
Microsoft's HTML Help compiler can generate a contents list. It generally does a poor job on HTML from web sites. If you are saving a site that you want a decent contents list for, you can edit the project files manually or use a separate application to generate it, then compile the project yourself.
The search data that the MS compiler generates seems reasonable, so you might find that worthwhile.
To produce a document that more closely resembles the original web site, you can disable the navigation pane display in the options dialogue, or choose to have the document open with the navigation pane closed. Both of these options are available on the "Navigation" tab.
You might like to check the Scrapbook data folder for a stored site before compiling and remove any files generated by Scrapbook CHM Creator and Scrapbook MAF Creator to avoid making the resulting file larger than necessary.
Multiple Compilations
You can also right-click on the folders in Scrapbook's sidebar and select "Create CHM" to compile help files for all sites stored in that folder. Project and help files will be created in Scrapbook's data directory for each site unless you have an output or log path set. Please note that the effect of using a log file path other than the data directory, for MS HTML Help Workshop at least, will be that the log is overwritten for each compiler run so that only the log for the last compilation in the series will exist in the log file on completion.