You'll need to use the TOC option in the conversion options. The options expect an XPath expression to describe what chapter headings look like. You'll probably want to use somethig like the following:
Code:
Layer 1:
//h:p[re:test(., 'chapter', 'i')]
Layer 2:
//h:p[re:test(., 'chapter', 'i')]
Layer 3:
//h:p[re:test(., '[a-z]\.\s', 'i')]
(Note that these expressions may or may not work, they're mostly intended to get you started. There's a
XPath tutorial available in case you need it. Also note that this might only work if there's no TOC already present- if there is, you'll need to force the use of the autogenerated TOC, see the TOC options page in the conversion options for that.)