You have a really complicated question here if you haven't done much genetics yet.

My college students get confused by Punnett squares too. It's pretty hard to explain them without showing them step by step.

I'll help you with the flies, though. Once you answer my questions, if you still need help, write back and I promise to help you with the squares.

Okay, so you have your first 2 flies and mate them. The parent flies would be P1 and P2. (You started with 4, but let's keep it simple.)

The next generation would be the F1 flies. I'll assume you're just counting the new ones, so your F1 generation would be 5 red females and 4 red males. If you then bred your F1 generation together, you got the F2 generation. Breeding your F2's together gives you your F3 generation.

Here's a table:
Parental: 2 red female : 2 red male
F1: 5 red female : 4 red male
F2: 11 red female : 0 red male: 2 white male
F3: 20 red female : 15 red male: 8 white male

Now here are my questions for you:
If a trait is dominant, can 2 parents with the dominant trait have an offspring with the recessive trait?
If a trait is recessive, can 2 parents with the recessive trait have an offspring with the dominant trait?

Once you answer these questions you'll be able to figure out whether red eyes are dominant or recessive.

Now you have to ask yourself whether the eye color gene is found on the X chromosome or some other chromosome. Male flies (like male humans) are XY. Females are XX. Males get a Y chromosome from their dads. The Y has little information other than telling him to be male. The male gets his only X chromosome from his mom, so whether it's the recessive one or the dominant one, that's the trait he'll have. While his sister will have two copies of a gene (EE or Ee or ee), he'll only have one (e or E). So males are much more likely to show recessive, X-linked traits. So what do you think, is eye color an X-linked trait?

Once you can tell me which eye color is dominant and whether the gene for eye color is on the X chromosome, you'll be ready to do your squares. Let me know if you need help.