does this mean that i can use the arduino motherboard (with the microcontroler disconnected) to connect the zigbee directly to PC via usb?
Yes, it does.
in which mode should i set up the zigbee-s then?
Can't help you there. I never was successful in getting two series 2 XBees to talk to each other. I could get one to send and the other to receive, but di-directional communication eluded me. I believe, though, that other here have reported getting them to communicate bi-directionally.