I am by no means a towing guru so I'm sure some more experienced hands will chime in on this as well.
It's been my experience that using the factory shipping points, attachements and/or hooks should always be utilized if possible. They were engineered into those spots for a reason and you'll be hard pressed to find a better point to tie onto the frame or undercarriage. Crossing the tie down chains/straps does have it's advantages though I can't seem to recall why while I'm writing this. The car should be placed on the trailer in a location that does give it a slight weight forward bias. I know there's a certain figure or chart to determine what the tongue weight should be and I wasn't able to find it. The weight of your miata is pretty low and the combined weight of the trailer and car will be well below your max so a tongue weight of 500 to 750 pounds with the car either centered over the trailers axles or with a slight forward bias is what you can expect. (Like I said... I'm not the towing guru but I've done once or twice).
I hope this helps and I also hope a few others will chime in here with their expertise to help you out. Good luck!