Amikoe schrieb:
Using InDesign CS6 (Mac):
I'm to start a 50-page document that's single-pages (not spreads) for a 3-hole-punch book. …
Exactly THAT is you problem!
Set up your document with facing pages and use 1 single master for the whole spread.
Set up, as I would recommend to do so with wire-O-binding which has the same needs as a punched hole binding.:
Further:
Don't use master text frames, except for placeholders for page numbers and living column titles.
Use Layers! Put your page numbers on the top most layers.