Yes, your speeds shown in uTorrent will ramp down to 0, they won't instantly drop to 0 when the VPN is disconnected. Same thing happens with Comodo, but the important thing is that your torrent client is not using your unprotected internet connection. You can check this from the firewall logs.
For your second question, that should be pretty self explanatory. Data is coming over the VPN, then pushed to your NAS over LAN.