Hi Jay,
The steps is the manual should work.  I have read the manual you are using.  I presume the step you are talking about is step 6.  That step is broken into two parts, 1 part for the DAQmx driver and one part for the Trad DAQ driver.  You should only carry out one of these steps.  I recommend using the DAQmx driver.
As for your 2nd question, you can send and receive handshaking and triggers through the backplane.  See the following links for more information.
http://digital.ni.com/public.nsf/websearch/37AF180CA4097DFB86256FF100513FB7?OpenDocument
http://digital.ni.com/public.nsf/websearch/68E619B9102D224F86256D880057A9C6?OpenDocument
Hope this helps,
Seamus