definitely take the clones before you change the photo period... you don't want to stress the cuttings, especially considering you're wanting to have them root...
what you need to do is:
1. take cuttings (2-3) from each of your plants and label them to keep track of where they came from
2. dip them in cloning solution and use whatever propagation medium you're most comfortable with
3. keep those clones under 24 hour photo period
4. change the original plants photo period to 12/12
5. wait to see the sex of the plants
6. throw out any of the plants that turn out to be male
as far as your concern of the male plants causing any problem with the female plants:
the male plants will have to produce pollen sacks and then release them into the air to pollinate the female plants in order for them to do any harm, this will take weeks after you notice the pollen sacks that signify the plants sex as male... so there's nothing to worry about there.
ALSO: if you only have one light, simply remove the plants from the light room and make sealed room, maybe a closet or something... and then put them back in after 12 hours... then repeat.
it may sound like a lot of work, but if you follow these simple steps, you will never have to do it again, and a healthy mother plant can live for up to 8-12 years... so it's worth it.. just make sure to never prune more than 50 percent of any plant at any stage of it's life period...
hope that helped. I've only had one crop, but i'm almost done with my second, about 2-3 weeks out... the first was fire though!!!!