Dirk, I hate to try to advise people on which fasteners to use on something I have not installed before
. You need to contact the mfg. on what they recommend using. Install it perpendicular and don't worry about hitting the joist, it won't happen anyway. If you hit a nail the staple will fold up or come back thru a board. Thats not a big problem.
Is this a solid or engineered wood? It matters, and does the mfg. say to leave that much expansion?
You can blind nail the starting rows without having to face nail everything.