A manuscript is simply a book that is in possession by the author, is going through changes, has not been published, and is not finished yet.
If you want to write a book, just write it the way you see published books written with chapters etc...
After you are done writing, you need to edit, edit, EDIT!!!!!!!!!!! Edit it yourself until you want to throw it against the wall, then give it to a trusted adult like relatives or a teacher and have them edit it. Put it away for 2-3 months, and edit it again. When you finally feel it's close to done, send out query letters to agents.
You will probably get rejected a number of times before you are accepted. If you manage to find an agent they will work with you on getting the manuscript to the publisher, which, I might add, will take a while because you will probably get rejected many times.
The key to all of this is to never give up, but right now, I would suggest you don't worry about getting it published and just write.