Red, some random thoughts...
Everything these good folks are saying is good advice.
It would help to read up on uboats and maybe even a specific boat. These uboatmen were the enemy of the Allied war effort, but they were proud sailors who worked too hard and about 80% died, all unpleasantly. Worth knowing abou them.
Limber holes - (floods and vents in non US sub talk). You can drill and cut (with VERY sharp #11 x-acto blade), but if you have or can borrow a Dremel tool, this really is the best method, a "work smarter not harder" thing. It's a matter of letting a grinding bit grind away the plastic (from INSIDE) until each hole becomes see-through because it's so thin. That's when you stop grinding and easily cut it out with the #11. Other methods work, but none are as fast and "easy" (a relative term). Do heed the advice of others and not use too much speed, melting is bad. For extra accuracy, use the #11 blade to make angle cuts on the side and bottom of each hole (just a few swish smooth passes) so that the edges are thinned very, very thin (or in Monty Python terms, "wafer thin"). This gives the illusion of scale-thickness metal and keeps some plastic strength.
Yankee P-hull - I've been polite before, but really, it's a piece of...notgood. As pointed out, you won't see it thru the deck, and it's expensive and doesn't fit well and not at all accurate. You mightwant to make a cone shape in the bow if you hollow out the bottom floods (can be seen), tho Modelbrass PE is the best way to go there.
Also as pointed out, if you do a mostly Out Of the Box build with some good PE, concentrate on painting and you should have a great looking build.
I'm a bit biasedso I'm going to recommend you spend heaps of money on some cool stuff: namely the Floods and Vents Phot Etch kit available from White Ensign Models (WEM) - that's a product Dougie Martindale and I design and released and sold to WEM. Dougie has a great article on authentic paint, and I have some various hints on creating your own, or buying paint from WEM.
As Accurate Model Parts (AMP) Dougie and I sell high-tech fabric flags and waterline and Snorting Bull decals. Because this is a school project (sounds like a cool school!) AMP will send you a free fabric flag to top off your build. But you have to earn it: you must read something on uboats, and also post some pictures of your progress, we'd all love to have a look!
Send me a message or email and we'll get you a flag.
AMP - Accurate Model Parts
Fabric Flags, AM Uboat Goodies & More
http://amp.rokket.biz/