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Sounds good to me. The goal is to make your system only as complex as it needs to be, and as effortless as possible to set up and maintain.

I would give each class its own folder. This way there is a persistent reminder of your commitment even if you have completed all current projects. It also allows you to focus on a single class ("focus", as in using the focus button in the tool bar).

When deciding what projects to make, keep in mind that the only way to make actions sequential is to put them into the same project. So, for example, you could enter all the syllabus assignments as actions into one project and then just work through them in order.

Also keep in mind that if an assignment can be done at any time and has more than one action step, it may be best to make a new project out of it, rather than tagging it on to a general "assignments" project. That way, when you view your work in context mode, it will be available to work on whenever you have the ability or opportunity, and you won't have to wait for an unrelated project to be done before working on it.

You may also want one Miscellaneous single actions list in each folder too, if you need it.

If something has more than 1 action step, it merits its own project. An exception is if the project is part of a sequential series of projects (like assignments, btw), in which case you can make them into action groups (sub-projects). It takes a little experimentation and use to figure out what works best for each situation.

By the way, have you read Getting Things Done? If not, you should do that as soon as you can.