I think you are worrying about problems before they happen
The usual way is not to use homebred males on your ewes until you have a sufficiently large number of breeding sheep that you can run separate 'lines'. Then you can have a number of separate breeding groups, using homebred males on unrelated females. This is what we do, and at the same time we buy in a fresh tup every couple of years to keep the bloodlines fresh.
As you haven't set up your holding yet, you can plan ahead to avoid a situation where a ewe is still running with her own son at breeding time, by having separate paddocks - separate the males from their dams and sisters at 4 months - after this age there is a danger, increasing as they get older, that the tup lamb will mate with his dam or twin. Reminds me of the old lady with two cats, male and female from the same litter. When the queen cat produced kittens she asked the vet how that could be. The obvious culprit was sitting right there looking proud of his offspring. The old lady said "oh but he wouldn't - she's his
sister ". Sheep, and cats, don't seem to have a concept of consanguinity. In Suffolks, using very few tups and AI in the 50s (I think) a huge problem with inherited disease arose which they are still trying to eradicate, so yes, inbreeding can lead to problems. On the other hand, there is a system called line breeding where matings with close relatives are arranged in order to 'fix' a specific trait in that line, such as fine fleece or extra size.
When you choose your first ewes, check their pedigrees and go for unrelated bloodlines which will give you a broad genetic base to start with. If you have only two ewes and each has twins, one of each sex, you could then run (breed) a tup lamb from one ewe with the other ewe (in separate paddocks), and vice versa but you could only do this for one year. We don't breed from one yearold ewe lambs but if you did that would be a problem, so best to plan on bringing in, buying or borrowing, a fresh tup each year. As I've suggested elsewhere, this can be a tup lamb which you then send off for the freezer after he has done his work