Megamart is more a warehouse style of shopping, kinda like Costco. Progressive is a grocery store. I prefer Progressive myself for groceries, veg, and the meat counter, but will go to Megamart if I need something other than groceries, like auto supplies, kitchen stuff, desks and chairs. Prices are about the same with the exception of booze. I find Megamart a little expensive.

A couple of tips though;
1. Not sure where you're from WpgAngle but if the Wpg indicates you're Canadian, Progressive has Clamato on sale right now.
2. The drive out of MoBay along Alice Eldemire Drive from the police station to the final turn towards Negril can be a nightmare, especially at rush hour. I'd go to Megamart, shop, and then take the road out of Megamart but towards Barnett Street and then out that way. Could save you from bumper to bumper traffic. If it's rush hour, getting out of Progressive and Fairview shopping Mall is even worse than the main road.