Pollinating right now is ideal. Seeds take 4-6 weeks to grow and mature, so will fit the time frame of what stage your plants are at now.
Apply the pollen with a small paintbrush, pollen sticks to Q-Tips too much. If you only have a small amount of pollen, you can mix it 50-50 with corn/rice flour to extend it. About an hour after application, spritz the left over pollen on the plants with plain water, this will kill the pollen and stop it fertilizing everywhere. It is also a good idea to tie a piece of string loosely around the pollinated branches to be able to identify them later. Write down the date of pollination too, this will remind you of when to start checking for seed maturity. Once matured, the seeds will become visible as the calyxes dry out to expose the seeds, so that they can then fall to the ground. Unless you are using pollen from a female that has been genetically mutated to produce feminized pollen, the seeds you breed will be regular seeds, meaning that they have a 50-50 chance of being either male or female. Hopefully you are not intending to use pollen from a hermaphroditic female, this will lead to seeds with a genetic dominance of being hermaphrodites themselves and they will not be feminized seeds, but regular seeds with a predisposition to being hermaphrodites and have a 50-50 chance of being either male or female.
Hope this helps,.............
Organoman.