Version 6 saves documents in files with the file extension .sci.  The .sci format is a .zip format file that contains the .xhtml format of the document itself, plus any imported graphics, and also the generated LaTeX files.

Use File, Import TeX to bring Version 5.5 or older .tex files in Version 6.

If you see the message "Please convert your document to LaTeX2e", see Error "Please convert your document to LaTeX2e" when using File, Import TeX.