Hello,
You cannot parallel two boards! It is one board at a time connected to a Cyclone, because the BKGD/MS pin utilises data transfer in both directions.
The previous comment made referred to the possibility for the Cyclone to operate stand alone, without the need to always be connected to a computer. This would simplify the use of multiple Cyclone Pros, but still only with a single board connected to each one at any instant.
Regards,
Mac