I don't want to use SiteBuilder to build my site within Yahoo Small Business Hosting and need to know if I can use my own web site template that includes server side include technology (SSI) for such items as a header/footer/menus/etc.

I don't know if they are expressly allowed but I do know for certain that at least the include file ssi tag works. however, it will garble stuff like Yahoo store-tag links so your mileage may vary.