I've been using Sigil so far to make epubs but i was wondering if there's any better programs i could use, preferably free but doesn't have to be, that would be more efficient. The bulk of the books i'll be making have a lot of footnotes, finding solutions to issues i have with Sigil is very difficult and time consuming so it would be useful to have something that's better known. Thanks
I don't know a lot about sigil, but I have made a book with footnotes, and I have been using an xml editor with docbook to generate an epub with footnotes. Works well.
Unless you're already fluent in docbook, I suspect you wouldn't want to learn that.
Adobe InDesign already has a functionality to convert footnotes into epub http://helpx.adobe.com/indesign/using/export-content-epub-cc.html#reflowable_export_options Indesign is a real bear, but the monthly rental rates for the software might make it a good option for you.