pc->arduino+xbee------------arduino+xbee->bot

I am trying to control a bot using arduinos and xbee s2 one arduino is
the transmitter which is connected to computer and other arduino is the
receiver the transmitter xbee is configured as Coordinator AT and the
receiver xbee is configured as Router/End Device AT the modems are
communicating with each other I checked it using X-CTU legacy version.I
think is is the arduino xbee shield is causing a ruckus (I use
ITEADStudios xbee v1.1 shield this specific one uses
jumpers[http://www.robotshop.com/media/files/pdf/datasheet-shd005.pdf]).I
tried
different combinations of this jumpers everything was vain.To be exact I
tried this thing in arduino
http://arduino.cc/en/Guide/ArduinoWirelessShieldS2 there was not a
single positive result.

Now my query is
1.Is there any way of connecting the arduino to the xbee module
directly?If yes please suggest any links.

2.Or if I could use the xbee shield directly the what will be the jumper
configurations?

3.And i came across something called hardware serial and software serial
what is it??

4.Is there a trouble with the aforementioned code of with my shield
which hindering my communication because of some lousy jumper
configurations??