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Okay in an attempt to recreate what you are seeing. I created an epub3 with a proper nav (ie. marked as "nav" in the manifest properties of the opf). Deleted it from the spine in the opf (you can NOT delete it from the manifest). Saved the epub.
Loaded the epub and the nav.xhtml was near the top (not at the actual top) when reloaded BUT was NOT part of the spine! So all is good. The nav.xhtml has to someplace in BookBrowser otherwise you could not select it for editing.
If I then drag the nav.xhtml to the end (as if I want the nav to be last in the spine), it will be re-added to the end of the spine as expected.
So to summarize:
In a proper epub3:
a) to put the nav.xhtml file last, simply drag and drop it there in Sigil's BookBrowser window.
b) to make the nav not be shown to the user, you have two options:
1) edit the OPF and add the fololwing to the nav spine entry:
linear="no"
This should tell every epub3 reader to not display the nav as part of the normal spine order.
Most epub2 readers unfortunately do not know how to handle linear="no" properly.
or
2) simply remove the nav entry from the spine completely (not the manifest!) before saving the epub
And if you do that you probably want to do what Doitsu suggested to edit the nav.xhtml Landmarks section first to that it will point the user to a html toc.
Hope this helps.
KevinH
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