Angie, welcome! This must be a difficult time for both of you, but you are doing the right thing by meeting with an ostomy specialist.
There are many people who will be along to give you some help. There are products out there to help build up creases/low spots, for better wear time...an example would be hollister's adapt barrier strips...Do you have a catalog for ostomy supplies? It might help to just look through the pages and get an idea of what is out there. You definately have "common sense" on your side with your comment about "building up the opening" not making sense (especially with a flush stoma)!!
Your dad is lucky to have you. Remember, no question is silly, so keep asking!
it's a great site...the link is www.uoaa.org