Paulycali,
I few things I've done that might be helpful....
I usually cut away most of the male, leaving just the top or a single branch, less to keep track of that way. Before he blows I take him to a closet with flourescents so he is isolated, or I have sometimes cut the branch and put it in a vase of water in a room with no air movement with glossy paper underneath. The branch will stay alive for a week or so, certainly long enough to drop the pollen...Last year I had branches like this that grew roots in the vase! I put the pollen I collect in a plastic film cannister, although these are getting hard to find since no one uses film hardly anymore. I use a small watercolor brush, or a Q-tip and apply pollen lightly to all of the pistils on a branch or two or three.
Some pollen will drift off, but I never have more than a few stray seeds that develop anywhere but the branches I am seeding.
Some strains will produce seeds extremely easily, some are harder to seed. Last year I used the same male to seed 7 female strains over a few days. Two or three strains seeded really well, two or three moderatly well, and one Deep Chunk/Stawberry Cough was exposed to much pollen but only produced one seed.
I've always done this outdoors on large plants, this year I am going to take some small indoor females and put them in an isolated room under flourescents with a male. Once they are seeded, I will put them back in the flower room to finish up the seeds.
Good luck....