Oh it took me a few weeks to beat them all when I faced them the firs time normally. You just need to keep on trying and trying, memorizing things from the bosses, their attacks and etc... Do not feel lost or hopeless!
You were brave enough to face the horror known as the gummi ship mission, something I still havent done to this day.
You just got to play the Gummi mission to unlock more items. The Missions have a specific requirement and when you're done. Just make the Donut Ship to burst through every level and you're done.