So you changed NOTHING else except putting in the larger amp and it got quieter? I'd guess either a coil isn't hooked up, you opened a coil, or there's something wrong. The RF amp should have that sub going pretty nice.
I would suggest double checking EVERYTHING. If it never smelled before and now it's getting smelly and not as loud that's really strange. Assuming it's the amp, it would be a very unusual sort of fault and frankly a company like RF would have protection features to shut it down if that happened, so I'd be looking more for user error.
Pics would help.... post to a photo-hosting site and paste links here in IMG tags.