Secondly, I currently pair some of the turnouts together such as on the double crossovers and on passing sidings so that they operate simultaneously. Do I need to seperate them for use with Rocrail or other PC control?
I believe you can use them together, there is some discussion here for Rocrail
http://forum.rocrail.net/viewtopic.php?t=385&sid=6c4e3c7381a2dff7716bb17be994eede
Using "actions" or "using a route" seemed to be the description of how to have it show correctly in the GUI (change one, both show changed position).