Hey Wayan,
MDF is very good for glueing, don't worrie about it!
You could just glue the whole box without screw, it would be a challenge to line the corners up and press everything well together, but the glue is realy strong and more then sufficient.
You do have to give it some time to dry of course.
To seal a side that has to be removable use weatherstriping, works very well.
When the lid is screwed on, it's almost invisible because it's pressed flat.
Or just put it upside down on a carpet, seems to play at its best this way
you need a flat floor, no bumpy tiles etc.
I made a few Velleman amps before, have a look at there website, nice stuff, not the cheapest though.
If you like to use a stereo amp:
Take the mono/sub out of your Yamaha.
Go to the input of the stereo amp with a splitter and feed left and right the same signal.
Then use one output side for one driver in your WO and the other channel for the other woofer.
happy building!

Bart
Particle board is weaker, maybe you should use those biscuits now, but that's more work and glue.
If you don't plan on dropping them from the stairs, it should be ok. ;D
edit: be sure to predrill holes for screw, specialy with paricle board.
If you use a lid, you should use those metal threaded pieces instead of just screwing directly in the wood.
Velleman dealer in India:
(maybe that's the nearest, so not a good solution for you?)
VPL Infotech & Consultants
301 Savitri Sadan II 15 Comm Centre Preet Vihar
110092, DELHI
INDIA