The folks at /r/AskAnthropology might enjoy this question.

If you're asking about incest itself, they 'knew how to do that' the same way we do. Incest taboos exist worldwide in some fashion; not only that, they appear in many ape species (bonobos a notable exception). Chasing that line of thought further would refine your question as searching for the origins of incest taboos, something definitely suited for the anthropology subreddit.

It's not likely that the clan elders came up with the idea -- rather they reiterated its enforcement as part of a generations-long tradition that may or may not have biological roots, even.

Also, anthropologists classify different kinds of kinship. A clan or moiety is usually considered an example of 'fictive kinship'. In the Native American cultures that prevent inter-breeding with clans, the clans typically take their name from an ancestral figure, either wholly spiritual or a physical person (albeit possibly legendary) considered to have existed so far back in time that genealogy is impractical. So if you were an Ojibwa in the Otter clan, you trace your ancestry to the Otter manitou. That would mean everyone else that does the same is related to you, hence the incest taboo.