I'm no authority on breeding animals, but have bred plants for a long time. It's usually the person who care enough about the breed/strain enough to preserve them. Have the little extra eye to detail, and know when a bad parent is just that.
		
		
	 
Good breeders; no matter what species; think the same. Just like plant breeding I suppose! I personally find it a shame if a breed like Indian runners would become extinct because everyone just breeds like "whatevs". It's throwing away hundreds of years of invested breeders-history! I sometimes peek at the chickens here; and am amazed. A lot of pupular chicken breeds from literally every tiny village around me are still bred in the U.S.A. We had a weird phase/fad a few 100 years ago where your tiny village only ment something with it's own chicken-breed. That was fashion and also some kind of contest; like competing soccer/football teams! That history is preserved by breeders all over the world :O (while you hardly can't find them over here anymore :'( ) 
That being said; that the preserving is also preserving history; that all is useless when you don't breed healthy. It's probably not different in plants. Allthough you want to preserve; putting the "preserving" above and chosing pretty but unhealthy plants for that will bite you in the bottom in the end; it will not last. Sometimes you have to have a bit of a setback and breed with uglier healthy ones to keep them healthy. 
I don't know any websites with basics for duckbreeding. But I think with these basic rules you can start your own; even from mutts;
- Never let family have offspring.
- Be 100 % sure who the parents are.
- Ring the ducks.
- Create an database with every ringed duck in it. Write down information about them.
- Keep contact information from the people your ducks go to; ask them to contact you when it died/is sick/ anything unusual. Contact themself regularly to ask how the ducks are doing.
- When you see a negative tendency in offspring like; dieing early for no clear reasons; having a lot of infertile eggs or chicks die in eggs, all a lot of stress, or any deformity that can harm the duck; quit with breeding with any family-member of these ducks; contact breeders with this information and ask them to not let that duck have offspring. 
- Make ethical dicissions. And don't hurry dicissions. Let's say; you want to create a breed that lay's many eggs. You have a duck that lay's 3 a day! Wait a year or 2 to see how this infects her health. And even after that; don't breed too heavy. Maybe it won't effect her in a year; but eventually it takes a toll after 6 years. That is more repairable with 10 offspring running around from her then 4000. 
- Keep your groups mental health in mind. That's probably different then plants. Well; too many plants planted together is negative for the plants; that's the same; but I keep the most ugly duck ever around because she is a GREAT leader. She has a positive stable effect on the group; hence more happy ducks and healthier ducks. She will not be a biological mom though; but removing this "mom" of the group will leave a disbalance. The same goes for having personality variety; sometimes you can't keep the prettiest one because it is headstrong and you already have too many headstrong ones in the group; or too shy and you have too many shy ones in the group. 
- Accept it costs you more money then you make of it 
 
I don't think it is very different from plants with the right morality.