I can answer that real fast. No they are not connected on the board. You will have to run Net Bridges to them in order for them to hook up to your main incoming power. You have to do this on the power side and the ground side as well. It isn't that hard to do. Just goto PLACE>Net Bridge and select one from the database. It will ask you which 2 nets are to be connected. Just select the net for VCC and the net number for the analog power and place it on the board somewhere. When you autoroute, then it will automatically hook the net bridge on the board to the appropriate traces. Do the same thing for GND and Net.
The other option is to hook everything back to the way you had it to start with in Multisim before transfering it. It won't simulate properly under these conditions, but it would make the transfer more seemless. Whichever technique makes it easier for you is the one I would choose.
I hope this helps.
