Two things:

1) For transport: I use wine diapers (you can purchase them on Amazon). They hold regular liquor bottles and wine bottles quite easily. Otherwise I use t-shirts to wrap around the bottles stick them in the middle. I've never had a problem though with transporting and any kind of limit or weight issue (apart from airline weight limits)
2) For declaring: I always declare the full amount of what I have because of my Global Entry (I would hate to lose it over a few dollars of duty). I have never actually been asked to pay any duty when I've exceeded the limit. The last couple of times they CBP agent has asked me why I was flagged, I've then told them I came from XYZ and had wine / liquor that exceeded the limit, and they've said okay great and waved me through

I have paid duty in Japan -- one time I was on a trip that took me to Australia and then back to Japan. I had wine that exceeded their limit and so they charged me something even though I was only there for 20 hours (I believe technically per Japan laws, I was considered a transit passenger so didn't owe duty but it wasn't worth arguing over like $20)