I store my pollen in the freezer and dilute with corn starch, lasts forever, I have 10 year old pollen that stills works as intended. Only takes one particle of pollen to pollinate and create a seed, that’s why I dilute it with the corn starch so too much pollen is not wasted.
I separate my males from my females, then when my male starts opening I put a bag over it and shake it. I continue to do that until they stop producing large amounts of flowers. After that I put it all in a small glass file and stick it in the freezer. When I pollinate I use a small detail paintbrush and just stick the very tip in it and lightly bush it against the buds I want to pollinate. I move my females to a different spot than the other females when I’m doing this, after a couple of days I lightly spritz it with distilled water to try to get the pollen to stay put and I put it back in my flower tent.
I have done both, early flower (3-4 weeks) equals a lot more seeds in my experience, whereas in mid-late flower (6-7 weeks) there are less fresh pistils to pollinate, just remember it can take anywhere from 3-6 weeks for your seeds to mature, really depends on the strain, but I try to figure out others experiences with pollinating that strain and try to get my seeds to mature just before my buds do.