newsbin.com

I have two data directories and I am running two instances of the same Newsbin install, using the two separate nbi files.
Is that OK or do I need to run each nbi file with two different Newsbinpro64.exe (in two separate directories)?

The EXE doesn't matter. As long as you run each instance with it's own NBI file and each one using a using a unique data folder you're good.