Sand butter smooth. Any crevices/knots will let water seep in, and blow the paint out.
You'd probably fair better with oil based everything than latex--especially if its going to be exposed to the outdoors constantly. Oil paint will be smoother as it evens out nicer, so that water will sheet off easier.
By the way, which parts are peeling? And what color did you paint it?
--In humid environments, with lots of sun, I'd imagine a black painted plywood box would deteriorate at a much quicker rate than one painted white. If the tops are peeling the most, make sure you put on a nice primer, and perhaps even modify your box with a slight slope. (Just put a 2x4 on end closer to the cab, to elevate it a bit, and promote water sheeting).
I recall (don't quote me) that oil will stand up better in most times, but in really hot and humid environment, a latex MIGHT fair better.
Hope this all helps. More details could dictate better answers.