Not that I claim to have any knowledge on the subject, but I would expect that the largest, healthiest-looking fish would be the ones to breed, unless you're looking to maintain a specific characteristic (color, pattern, etc). If you're looking to sell them to your LFS, however, they'll pay more/give more store credit for the big, healthy ones first, I think. Otherwise I would say it's a matter of personal preference.
Thing with swordtail is you need bigger tank then you would need for guppies so it is a little more costly I think. Best thing to do like mentioned before pick out your healthiest fish get you a 1 to 2 ratio of the color you like or want to maybe mix to develop your own color and put them in a spawn tank and just let them go and keep breeding the generations by picking the best of the bunch. I have done this with guppy fry and made my own color it took about a year to develop a strong and healthy strain of a new guppy. Of course I have a nice size pond which is great cause I throw the fry in there and they grow SUPEr fast and it makes the process go by faster. I hope this helps you if you need more detail or have any questions I will be glad to help. I have not selectively bred swordtails but I have done guppies. If I can find something I'd like to take pictures to show you the strain I developed.
Mine are growing slowely. They are healthy, though, and I've only lost a few to stillbirth and more then 10 that got squished between the net and the supports.
