There are actually three types of Manhattan classrooms:
"Normal" courses - These are classrooms that are tied to the centralized login system. Users login using a single username/password form and then are presented with a "My Manhattan" page that lists all of their courses. They can then enter any course on the list.
"Standalone" courses - These classrooms are not connected to the centralized login system.
"Template courses" - A "course template" is intended to be a place for a teacher to "permanently" store course materials for re-use.
"Normal" courses are the most common type of Manhattan classroom.
A normal course is one that is connected to a central database of usernames and passwords. The login instructions in Logging In and the description of the "My Manhattan page" in The My Manhattan Page assume that each user, student or teacher, has a single username and password on the Manhattan server. When they correctly enter both into a form that your server administrator has provided, they'll be presented with a list of all the courses they are enrolled in on a "My Manhattan" page.
In a normal course, changing your Manhattan password within one classroom changes it for all of your classrooms. When you add a student to a normal course, (see Add a student) you are first asked to enter the student's ID number. Manhattan then looks up the student in the central database to determine if the student already has an account or not. Normal courses use centralized usernames and passwords.
A "standalone" course is NOT tied to the server's central database of usernames and passwords. They do NOT appear in your list of courses on your "My Manhattan" page.
A standalone classroom must be accessed via its own web address. Typically your server administrator will maintain a list of standalone course links at a web site. You'll go to that site, click on the course you want to enter, and be presented with a username/password form, which will get you into only that course.
Changing your password in a standalone course changes it for that course only. It does not change the password for any of your other standalone courses, or for your centralized Manhattan login you use for your normal courses.
Why use standalone courses?
Standalone courses are useful because the teacher (or system administrator) of a standalone course can freely add students or teachers to the course using fake names or student IDs, since these names/IDs are completely independent of the centralized system. This makes them useful for any application where you don't want or need to add students and teachers to your central list of Manhattan users, including:
Practice courses. If teachers are given a standalone course, they can play with Manhattan as both a student or a teacher, and can freely make up the names of students along with their ID numbers.
Clubs and other organizations. A standalone classroom could be created for a school club with a student as a teacher.
Besides the fact that standalone courses are not tied to Manhattan's central database of users, they look and behave exactly like 'normal' courses.
A "course template" is intended to be a place for a teacher to "permanently" store course materials for re-use.
After your first smashing success teaching an online course with Manhattan, you will have lots of important lecture notes, handouts, PowerPoint presentations, discussion starters, etc. in your current active Manhattan classroom. Your server administrator will certainly want to delete that course sooner or later, to free up disk space on the server.
The solution is to ask for a Course Template for that particular course, and use Manhattan's "Copy and Paste" feature (see Manhattan's Copy and Paste Commands) to copy your important course materials from your current course into your course template.
A course template is like a normal course in that it's connected to the centralized login system. That means your course templates will be listed along with your other courses when you login to Manhattan:

Course templates typically have one member - you, the teacher who owns the template. (However, there's nothing to prevent you from adding additional students or teachers.)
Certain modules are not available in course templates. These include the Post Office, Chat, Team and Anonymous discussion. That's because these modules don't make sense in the context of a course template. You'll also notice that course templates use a different background image on the Main Menu to remind teachers where they are.
Manhattan messages are copied to and from course templates using Manhattan's Copy and Paste feature (see Manhattan's Copy and Paste Commands.) A useful tip is to open two or more classrooms in separate web browser windows. From the "My Manhattan" page that lists all of your courses, click on a course link with your RIGHT mouse button and choose "Open in New Window" from the menu that appears:

You can repeat this to open as many courses as you wish at the same time. Now you can open a message in one of the open courses or templates, and click on the "Copy this message to my Clipboard" button near the bottom. Then you can switch browser windows to another course or template, start to post a new item in the appropriate module, and click on the "Paste message from clipboard" button to drop the message, along with any attached files, into the form.
Since Manhattan's Copy and Paste works on the server, you can quickly transfer megabytes of course materials to and from a course template in minutes, once you get a hang of the technique. Combined with Manhattan's ability to schedule topics for release at a certain date or time (see Teacher hidden and scheduled topics), you can load up a new course with all of the materials you've saved in your course template, and have it run on auto-pilot!