Andrew beat me to it.
I did a decent write up when i did mine...
http://formulaboatsforum.com/VBFORUM/showthread.php?6552-45Y-stereo-upgrade
they are all 6.5", and the only depth issues i ran into were on the arch speakers as Oz mentioned. I got rid of the u-bolts that get in the way by using straight bolts, and ended up with plenty of depth.
i don't think you can go bigger than the 6.5's though due to depth in the forward ceiling speakers.
personally, i went with WetSounds speakers because i thought they had the best sound...and I added a JL audio tweeter for each speaker in the cockpit. then i swapped the Kenwood amps for WS because they had loads more power. it was audible to say the least. i didn't need any more bass for fear of the boss, so i didn't try another sub. i thought one under the aft couch might work really well though. that would be truly free-air, and subject to the heat of the engine room.
the amps are under the couch down below. the center section.
also, the single best thing you can do for that stereo is re-wire the speakers IMO. they're all part of the single wiring loom and run right past the circuit breakers. once i upgraded the amps i had massive ground hum, and no amount of gadgets was able to solve it...nor a direct ground to the house batteries.
best of luck and congrats on the new boat!!
Todd