I have also two PXI-6025E Multifunction I/O -cards which would maybe more useful with counter outputs.
I think I understand what you are trying to do. Essentially you have two counters, but you want to be able to control their phase relationship to one another. This is definitely possible to do; however, there are not many examples dealing with it.
I did find one Traditional DAQ Example (non- M-Series) that might help you out with this: Twin Pulse Train Generation with Variable Phase Shift Control
Traditional DAQ uses an older API, so I would recommend you look at the attached example over this example. Just wanted to give you more than one option.
As far as it 'counting' up or down, that really would have to be done by a counter input task. Since the input would be the same as that for a quadrature encoder, then you would use the methods described in my previous post. As the output it will simply look like two different counters.
For the best solution though, I went ahead and created an example for you. It shows how to generate 2 different counter pulses that are out of phase with one another by a specified amount of time.
Hope this helps,