I'm also confused as to the effect of the referendum. Would this have overturned the federal ruling if voters had voted "no" to marriage equality?

Yes, ultimately the people have the power in Switzerland. Though the houses of Parliament still have the final say in how a law is implemented. Basically both houses voted yes, with the majority of opposition coming from the right wing faction (3/4 voted no) that would be parties like the SVP (People's Party), Lega Dei Ticinese and the party that actually brought the challenge the EDU, who split from the Protestant party, because they weren't Christian enough

One of the people who put the posters up is Oskar Freysinger, who's a fairly notorious shit stirrer on these sorts of things. Ultimately though the referendum was accepted with a majority in all cantons, including the more conservative rural ones.