Many thanks to those who responded to my plaintive “Lost in compile” post. With their help and iterations through the manual, video tutorials, and trail-and-error, I’ve found a path out of the wilderness.
I am working on a book with chapters, first-order headings, second-order headings, etc. Headings are formatted with styles. Pretty simple, but I was flummoxed about how to fit this into compile and choose my own fonts and so forth. For anyone else with a non-screenplay 
manuscript, stuck on the same issues, here’s a very short summary of what I did to get what I wanted.
–Under Project…Project Settings define two Section Types, Chapter Title and Text. Default Types by Structure was set such that Level 1 folders are Chapter Title and All file groups and All files are Text. (Level 1 folder names are chapter titles and contain text docs that make up the chapter)
–Under Compile define a new Project Format.
–Double-click new format to edit.
–Under Section Layouts delete all the defaults (-) and add two new ones, Chapter Title and Text. Former contains Title only (check that box), latter Text only. Save.
–Under Section Layouts select Font is Determined by Section Layout.
–Click Assign Section Layouts and make sure Chapter Title and Text are correct.
–Double-click format to edit it. Click Formatting tab. Select each layout type and format as you like.
Key realization for me: formats of the various headings (and captions, etc.) will carry through to the compiled output. These headings are not Section Titles in the compiler–they’re just text.
Really not so hard, but I was stuck for awhile and hope that this post might help anyone in the same situation.