Moving her to the breeding tank can be stressful. Keeping the lights out can help, and making sure there is some cover, a bit of plant or something. Some fish just seem to freak out when they're in a small container.
Do you really want to keep all the fry? If you just want a few, get some java moss (off the internet if your local shop doesn't stock it), put it in your main tank and leave her there. Most of the fry will get eaten but you should get 2 or 3 from each batch - soon multiplies! After you've been through this once or twice, you'll get a better idea of how to tell when she's due, and then if you want to take her out you'll be able to time it.
Good luck!