Hi jasn009,
Are you asking if you can replace a PCI-DIO-96 with a PCI-6509?
With regards to the hardware, they both work with the SH100-100-F cable, so the hardware form and fit should cause no problem. I believe the pinouts of the two devices are similar but you can check the Digital I/O Connection Diagrams in the User Manuals for the <a href="http://www.ni.com/pdf/manuals/372117a.pdf" target="_blank">PCI-6509</a> and the <a href="http://www.ni.com/pdf/manuals/320938c.pdf" target="_blank">PCI-DIO-96</a>, along with the <a href="http://digital.ni.com/public.nsf/allkb/862567530005F09F8625688600578509?OpenDocument" target="_blank">Knowledge Base</a> to interpret pin assignments, to ensure that the pins you are using are the same.
With regards to software, while the PCI-DIO-96 could be programmed with both Traditional NI-DAQ and NI-DAQmx, the PCI-6509 can only be programmed with the NI-DAQmx driver. If you have programs written with Traditional DAQ, you will need to replace the DAQ calls with the DAQmx calls. This tutorial entitled <a href="http://zone.ni.com/devzone/cda/tut/p/id/4342" target="_blank">Transition from Traditional NI-DAQ to NI-DAQmx in LabVIEW</a> will help. Hope this explanation helps, Mallori M