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Your use of the term bookmarks confused me. The actual terms are a Table of Contents (TOC) and Landmarks (Guide items). A bookmark is a user generated remembered location.
In an epub3, no toc.ncx is needed. Both its role and the opf guide are subsumed into the nav.xhtml document. But if you want older epub2 only readers to show a table of contents and guide/landmarks in your epub3 you can add them back.
In Sigil under epub3, the Table of Contents (TOC) tools work with the nav, not the toc.ncx.
There are tools in Sigil to create a TOC from the h1-h6 tags in the files. There are also tools to edit the TOC, promote/demote, and edit titles.
To set Landmarks/Guide items you use the Set Semantics tools by right clicking on a file in Sigil's BookBrowser.
Once you are happy with the TOC and have set appropriate file level semantics (which fills in the Nav landmarks info). You should be good to go for epub3.
If you want to create an epub3 that is more backwards compatible with older epub2 ereaders, there is an Epub3 Tools menu on Sigil that will create an equivalent toc.ncx and fill in the opf guide items.
There is also an epub3 tool menu to remove the toc.ncx and the opf guide if you do not care about being backwards compatible with epub2 only readers.
All of this is explained in the Sigil Users Guide.
Hope simething here helps.
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