I don't know what tut bren refered to but it looks like you did not delete or disolve the 2 edges in the middle of the top first. Delete them and then delete the top face. It needs to be one whole face on the top to get the hole, whole. Sorry for the bad pun.

Now the materials, from how it looks, you have all those mateials named. I can't see the image very well, to small. But, you should only have had 2 materials listed. If you look at my tutorial, you will see that I named them blue and pink and just assigned them to the proper groups and deleted all the extras. You would call them Green and red? But the brighter colors like what I used, shows up better when modeling. It does not have to be the same colors as mine, just use lighter colors..