Breed them. Find out which genetics you want because depending on which plant is which sex can alter the results, certain genetics that you are interested in carrying on to your hybrid might not actually be present in your results. Certain genes are recessive and some are dominant, you might end up with a White Widow with lowryder growth characteristics or you might end up with a normal photo period dependent plant. To mate 2 plants you should grow a male of one plant and a female of the other, keep them apart. Take clones from the female and grow to sexual maturity. Once male is mature harvest pollen and fertilize your female clone. Female clone must be flowering. Make sure you keep your male, female and clones separate so that you can harvest your females buds later. Female clone will produce seeds which contain your possibly successful new plant. Most of the difficulty I have gathered from reading about doing this is choosing the right strains to combine. Certain genes may produce hermaphrodites when combined.
Breeding autos requires true breeding techniques. If you cross (not breed as that suggests multiple generations) two strains, you'll get a hybrid. Hybrids are often vastly superior to either parent, but they don't breed true. The most awesome hybrids often make shitty offspring. To have a true breeding mix, you have to breed it until you weed out all the bad things... doing this, you lose the hybrid vigor and never really get back to that first awesome hybrid cross. If you're not breeding autos, you can take the best hybrid of a cross and just clone the shit out of it... -Loki