Chicago Manual of Style chapter and section title capitalization Ploughing through Chicago Manual of Style Online, I can't seem to find any concrete reference to whether chapter and section/subsection titles are capitalized in headline style or sentence style. 

It seems, given some examples that claim to follow CMoS that at least Chapter and first level Section headings are headline style, however, I'd love to find an authoritative statement from the Manual itself, but I can't find it (I'm referring to the actual manuscript, not to citations of book chapters, which should definitely be headline style).
If your publisher has its own guidelines, follow them. Otherwise this is described rather clearly in the "Manuscript preparation, editing, and proofreading" chapter of the Chicago Manual of Style. Their definition of 'manuscript' includes both books and journal articles; and 'subhead' means title or heading of any subdivision of the text below the chapter level.

CMoS 16th ed., sec. 2.55 on Editing part titles and chapter or article titles.:


  Chicago recommends that all titles be in headline style unless a work is part of a series or journal that follows some other capitalization style (see 8.157).


CMoS 16th ed., sec. 2.56 on Editing subheads:


  Chicago recommends that all subheads be in headline style unless a work is part of a series or journal that follows some other capitalization style (see 8.157). But if an author has consistently used sentence style for subheads (see 8.156), that style should not be altered without consultation with the author and publisher, since it may be more appropriate in a particular work. Where subheads consist of full sentences, sentence-style capitalization is preferable.