Just rub the clumps apart gently so drying can continue. A simple soaking for 24 hours will release the seeds and separate the fertile from the infertile ones. Cut the fruit open and remove the seed cluster to enhnce the releasing process. Pour off infertile seeds and once again collect the seeds that have sunk into a strainer. Lay them out to dry as you did with the tomato seeds, but be careful not to overexpose the seeds to the hot sun.
Chile seeds are less sun tolerant and prefer partial shade.
Once you have observed a full cycle or two of a given plant, you'll develop a feeling for its optimum placement in the garden. Irrigation of seed crops requires close attention to the maturation process. Be careful not to water when seeds are maturing or exposed and open. If irrigation is necessary, do it after picking sequences, not before. This is true with fruiting crips such as melons and tomatoes too.