Dietmar,
Assuming you want to setup the encoder all in HW,
For CTR0, connect UP/DN to DIO6.
For CTR1, connect UP/DN to DIO7.
You can also reference this very detailed application note on using encoders with DAQ STC(the digital chip on our E-Series boards)
http://zone.ni.com/devzone/conceptd.nsf/webmain/6F25CBA2CD73417786256869005E5FC3?opendocument&node=DZ52326_US
This should do it for you.
Kevin R