Pollinate all 3, but do a targeted pollination on lower branches with a brush instead of letting the male run wild in the tent. This gives you seeds from every pheno while keeping your main top buds seedless (sinsemilla) for harvesting and testing.
Budget Breeding Tip: Collect the pollen, let it dry for 24h, and mix it 1:1 with cornstarch (or oven-sterilized dry flour).
This is a classic botanical trick used by breeders: the starch acts as a natural desiccant to stop pollen from clumping, dilutes it so you don't waste precious genetics, and makes it visible on the brush so you don't accidentally dust the entire tent. Easy control, max results ;)