Should I cook my pasta completely if it's going in the oven after?!
If it's only going in the oven to get the cheese to melt, you can just cook it to al dente (instructions should be on the box).
If you're going to put it in the oven for a longer period of time (20-30 minutes), I would recommend cooking the pasta a minute or two less than recommended on the box for al dente. This would be if you want to brown the cheese a little rather than just melt it. This will also allow some of the sauce to absorb into the pasta and let the flavors all start to work together and be yummy. The choice is yours.
If you only want cheese melted on the top then fully cook the pasta. Place under the oven's broiler to melt the cheese. However, if you want more of a casserole/lasagna consistency to the dish, then only cook the pasta to about 75% doneness (soft on outside but still crunches on the inside), drain, add sauce, mix, add topping, cover with foil, bake at 350 degrees for 30 mins sauce will bubble, remove foil for last 5-7 mins of cooking time to brown it up. The sauce will finish cooking the pasta to perfection in the oven.
I'm not familiar with this dish from Pizza Hut so it depends on how long it's in the oven. If you're just going to melt cheese I'd cook the pasta all the way. If your using the oven to heat the dish thoroughly then I'd cook the pasta about 90% like you mention. Just make sure there's plenty of liquid so the pasta will finish cooking and doesn't dry out. A tip is to save some of the pasta water to add in case the dish dry starts to dry out in the oven.
I make baked pasta dishes all the time, and in this case you would cook the pasta all the way through. Cook your rotini til done, toss with your marinara, place in a casserole dish and top with cheese, then place it under the broiler for 4-6 minutes just long enough to melt the cheese. I would add a little of the pasta water (maybe 1/4 c) to the pasta and marinara before placing in the casserole dish because it will dry out just a little even with such a short time in the oven. sounds yummy!
i would cook it completely due to the fact that while it is in the oven it will not cook much more depending on what it is with, soups or like vegetables, but while in the oven it will get harder so the primary portion of cooking the noodles should be done prior to putting it in the oven.
It's your preference if you like your pasta a bit chewier then take it out a minute early but not any earlier then that because you want your pasta to fully cooked through, if you follow the time suggest on the box exactly that's fine too as it will not cook much more in the oven, the oven mainly will melt everything together.
I think you should cook it completely. It's probably not going to get any softer in the oven.
go with 90%