The technique to maintain distinctive breeds or even best of breeds for your area (largest fruit, most fruit, strongest grower, etc) is fairly straightforward for insect-pollinated plants.By what I've read, pepper plants (like tomato plants) are capable of self pollinating themselves and will on their own natural coarse.
Cross pollination occurs when bees (or other pollinators, such as hummingbirds and butterflies), pollinate one of the plant's flower with pollen from another plant of the same family (such as a nearby pepper plant of another variety). Wind can sometimes even blow the pollen from one plant to another. So, when multiple varieties of peppers are planted near each other, there's a very high chance that some of the flowers will have been cross pollinated, and therefor carry hybrid seeds.
Now it would seem unlikely that all of the flowers were cross pollinated, but the trouble (when trying to collect only pure seed) is that you can't tell which peppers carry pure seed, and which carry a hybrid variety.
- Before the flower opens, enclose 2-3 buds in some kind of bags to protect them. I like organza bags which are see-through, but can keep the bugs out.
- When 2+ flowers open for the desired plant, remove the bags, use a q-tip to manually pollinate back and forth between the two flowers and re-cover.
- When the flower dies and the fruit is growing, then you can remove the bag, but mark the specific fruit (I use a ribbons), so you can harvest them for seeds later.