Mega cone is not in the same league as going through PA. I play regularly with a drummer with a mega cone and whilst it's better than nothing, he'll still push for the PA. If your observation is that the kick drum is sounding like it's coming out of the PA, then I would wager your subs aren't much cop.
The success of getting your bass drum to sound good through the PA all depends upon your gear. First of all, you need a good sub... but secondly, you need some fairly powerful eq and critically, a compressor. Digital desks win here. If your EQ options are limited, an Audix D6 is a pretty good mic to go for - as it's naturally EQ response is pretty much where you want to be. You'll still want that compressor though...