There is no in-game quest tracking or notes section. If you want to solve the game without extensive use of the cluebook or online guides, you'll want to take notes for everything you come across. There is an automap feature built into the game with the Cartography skill (I believe MM1 is the only game in the series that doesn't have this to at least some degree)
The cluebook includes maps for every area of the game, so you can just print those out and then add notes where you see fit. There are no timing/text scrolling issues with DosBox, so it just works right away. Here are a few points (good and bad) specifically about MM2 to consider: This game has aged very well, and is still highly accessible and fun. I'm having a *grand* time playing it, and highly recommend it to everyone who picks up this package. I just wanted to give everyone a heads up about MM2.