1. If you can swing the VR3s, you won't be disappointed if you liked the sound of the VR2s.
2. You'll want the bass predominantly handled by your sub unless you have particularly capable towers. The VR3s are good down to 40Hz, so you can do both if you prefer. I run my VR3s large w/the Outlaw ICBM w/the crossover set to 60hz only for multichannel music (DVD-As, SACDs, etc) which allows all the bass down to 60Hz to be output from both the mains and sub, but for movies an all other source, I use the receiver's crossover setting of 80Hz and run them as small, diverting anything under 80Hz to my SVS.
3. You'll want a powered sub, powering a passive sub w/a receiver would be very hard on the receiver and due to most subwoofers being active (w/amplification built in), this will be your best option. I would do some critical listening for a few weeks w/the new speakers before deciding if you want to add an external amp to your setup as you may not need it. -TD