I would just leave alot of floating and plants at all levels for the babies to hide.Stack rocks or make a cave area for them to hide. When your guppy is done having them take her out of the tank. That's a good idea to have her in a 2.5 gal. tank to have the babies. I just kept an eye on mine through out the day and when I noticed that she was skinny again I took her out and put her in my main tank. I kept the babies in a 2.5 gal til they got bigger and not fit in the guppies mouth. feed crushed flake food.
Here is a good web site I saved under my favorites:
On the left hand side they have a section about pregnate guppies. The story on how she got started is sort of funny. Good luck with the babies!