You have to turn off "Smart Quotations" in the settings. I was specifically referring to Google Docs, which is the way I do things, but Word has the same setting. I suggest using Google Docs and just turning off Smart Quotations. I don't use Word nowadays because the Ribbon is dumb as fuck and OpenOffice is free, but I can rustle up a copy to see if I can lend a hand.
As for hte update you referred to, I would suggest you float it as a full thread. Making changes that significant through SCMS is rather frowned upon, as it prevents major changes from being run through the full process. Since it was just largely copyediting stuff, I'd be fine if you just autotagged it with Copyediting and ran it through. I just want a record somewhere.