I bought mollies when I first started the hobby month out a half a year ago. They breed like crazy. I usually let Darwinism play its course so I don't get too many. If you do want to try to keep as many as possible, here are the things I look for when I think my fish is about to give birth.
The pregnant Molly will start to "square off" looking like a rectangle. You can see an image here: http://i290.photobucket.com/albums/l...Mom38_1024.jpg
Second, I look for the gravid spot. Near the anal fin, the skin will look black and will get larger the closer to birth. You can see an example here (same fish as before, different photo/angle): http://i290.photobucket.com/albums/l...Mom41_1024.jpg
Third, the birth canal (white tube) will start to show the day before, mind you it is relatively small.
Fourth, the day prior the female will be swimming back in forth, or up and down, in the same line. I also notice the males pester her more. In my tank, the other species of fish gather too because they know food is coming.
Finally, the female will isolate herself in a corner, under rock, in a cave, behind some plants, etc. to avoid the attention from the other fish.
Like I said I let nature run its course, but for you, try not to put her in the breeder box too early. Not because its mean, but because she can get stressed out, have a miscarriage, or die.
You can reintroduce the fry to the tank as soon as they are too big to fit in any fish's mouth or get sucked in to the filter.
If you miss putting her in the box in time, try to catch the fry so they don't get eaten. Most stay on the bottom for a while, but some head to the surface. Make sure there are enough hiding spots in case you do miss it. Also, if she gives birth in the tank, check to filter to see if any got sucked up. There are some food birth videos on YouTube just for enjoyment to watch the miracle that is nature.
Hope this helps!