You'll want to read both channels in a single task and then split the data to your required VI's
This is a good, simple example.
http://digital.ni.com/public.nsf/allkb/0C1ADEF06A54AB2D862575040066FD51
Here are some other good DAQ related tutorials!
http://www.ni.com/white-paper/5370/en
http://www.ni.com/white-paper/5468/en
You may try looking at some design patterns. I would start by acquiring data in one loop while doing work with that data in a second loop.
http://www.ni.com/white-paper/11805/en
If you do some digging, you will find that many more Design Patterns on NI's website.
If you this still doesn't answer your question, post some code!
Good Luck!