Running the reading and writing in separate loops should not be a problem. You just need to make sure that you configure the ports first. In most cases, if you configure a port or line it will reset the other ports or lines. In this case make sure you stay away from the easy VIs like Read from Digital Line, Write to Digital Port, etc... I would recommend using the intermediate or advanced VIs. There are several examples that use these advanced VIs, or you can open the Easy VIs and copy the code from them. You just want to make sure you configure everything first, then you can write or read as much as you want.
I hope this helps.
Joshua