All components I use are from Master Database. I use rated virtual because they are simpler and its less work to place and modify them. Resistors from the resistor library will give you a more realisticall results and has extra options. Primarily you can set tolerance and faults. In most cases there is no difference between rated and rated virtual components unless you actually need those extra options.
Those aren't wire numbers those are net node names. Every time you place a wire a new net node is created and numbered with a next available integer. Double click a wire to see its properties and you can change its net name. If you have 2 wires that are not connected and you set them to have same net name they will be connected to the same node. There is no difference between a line and a dot other than a visual representation, it is all a single node. You can see it clearly on the schematic, everything connected to ground has a net number 0.