Yep… there is a learning curve to this… If you connect to a pin (i.e. GND) that belongs to a group, your air-wires will snap to the closet GND pin… If you move the parts around, the air wire will jump to the closest GND pin. The same thing happens when you complete a circuit. If move the parts around in the other views, the air-wires will jump around to the closest pin/part in that circuit. Once you change the air-wire to a hard wire it will remain in that position.
Just because the wires in the breadboard or pcb view are not connect to the same point (connector) in the breadboard vies does not mean the circuit is wrong i.e. the GND wires may run all over the place, but in the schematic view you my just want to run them to a GND symbol and accomplish the same thing.
Start moving the parts around the screen and watch your air-wires jump to the closest connect point it that route. You can then arrange the parts in the schematic view and change the air-wires to hard wires. The same thing applies in the pcb view… the air wires will jump around as you move the parts around, but once you run the trace everything will stay put.
I believe the preferred method is to start with the schematic view… that is if there is a preferred method… I think everyone has their own preferred method… When designing a circuit it general starts on paper… then to your breadboard for testing… and finely your finish product (your custom pcb)… Although, no one does it that way. I usually start with the pcb and then go to the schematic to make the pcb work out. .
Start moving stuff around in the different views and connecting hard wires and traces… you will get the hang of it…