ow do I write query that will refer to the data source if im writing a query in the project root?
See this example. If your table is called [My Table] and it is found within a DBM that you have linked into the project with the name [My Big DBF] then in a query that you create in the root you would call it [My Big DBF]::[My Table].
The example shows use of a read-only data source, and a query written in the root of the project.
For a different example see this one. That shows use of a read-only data source that is a web server providing images. It shows how to copy an image and paste it into the root, alter the table it uses to being the one within the data source, and thus converts a read-only thing into something for which the properties can be altered to change the styling.
The current build is 167. Download and install that. It is a regular Windows installer thing that installs Manifold within Windows so you can launch it from the Start button, etc. I personally much prefer the portable installations, since then you don't have to mess with Windows installation idiocy.
About the "create a new project from the installed build" - That's just a different way of saying "Install the latest build of Manifold, 167. Launch Manifold." He's just saying "make a fresh start."
When you launch Manifold it automatically opens up with a new project. You can then link in your DBF and do what you want. See Getting Started:
"Launch Manifold:Launch Manifold and it opens with a new, blank project. "
It's a shame your first experience with Manifold has run into something that gives you read-only access to that DBF. When you are learning a new thing, especially when trying to "wing it" by just applying the thing without reading documentation in the recommended order, it can be really annoying when you run into something like that. In truth, Manifold is pretty easy to pick up for many people even if you "wing it" but not if extraneous things like Windows preventing you from using files pops up. Usually, as the many examples and videos show (see the Gallery page) you just link stuff in that you want to use and Windows isn't going to interpose security measures to save you from yourself.
That "read only" deal is almost certainly something related to Windows security measures, which, of course, are a critically important feature in Windows, one of the many things Windows does in an attempt to prevent people from hurting themselves. You can get around such Windows features quite often in a brute force way by using Run as Administrator when you launch Manifold. But all that is a Windows matter, not Manifold.
Speaking of baffling Windows matters designed to prevent people from hurting themselves, if you've downloaded the DBF from Internet it could be that Windows has, of course without telling you, marked it as a blocked file that should not be used because it might be dangerous. You have to "unblock" it before Windows will let you use it.
One more tip: try downloading some of the example files from the Manifold product downloads page and working through the examples that use them. That will help you get your head around the basics in an efficient way, so that when you run into something abnormal that Windows throws at you, you'll have the confidence to know it is not something arising from your unfamiliarity with Manifold but, instead, a routine matter of something weird being tossed at you from Redmond. :-)