Jeff -
Unlike Fred, I do drive mine into the plywood. The "secret" is you need a nail-set (a piece of steel flat on one end to hit, with a small cupped point on the other end into which the nail-head settles). Home Depot sells a nice packaged set of three in various sizes: They're colored yellow, black and red. I use the red one for track nails.
I use cork roadbed, so I push the nail in, the cork holds it in place. Then I tap them in with a small hammer (7oz.) until they're firmly into the plywood, then finish with the nail-set. Yes, you must be careful or you will bend them or drive them too far, but it take not-much practice to develop "the touch"
Fred's suggestions are all to the good as well -- I've certainly done it that way with great results. If you're laying the track directly on plywood (which I personally don't recommend), then his way may be better -- not having a roadbed or cork, homasote or similar to hold the nail in place makes it much harder.
In the end I've simply found it's far, far faster to just nail them in -- IF you are good enough with the nail-set...
Kris