I’m not wholly clear what you’re after here.
When you say you want to pick and choose files to to combine together in one document, do you mean so you can edit them all together, or so that you can print them all out as one document?
a) Editing multiple documents in one go.
You can simply cmd-click in the Binder on as many documents you want and they will all be temporarily linked together in one big virtual document (called a ‘Scrivening’). This will work no matter which level the individual documents are on. If you click on folders, then the text of all their subdocuments will also be included.
Once you’ve chosen the documents, you may have to press cmd-1 once or twice to make sure the multiple documents are in the editor. (Cmd-1 toggles between View > Document and View > Scrivenings mode).
Once you’re in the virtual document, you’ll see that individual files are divided by a thin black line. You can have the title of each document appear or not with View > Editor > Show Titles in Scrivenings.
To add them all to a collection, so that you don’t have to select them every time,
First create a new collection (View > Collections > Show Collections, then press the plus sign in the Collections view header bar).
Secondly, click on the Binder heading to make sure you can see your documents, select them and drag them up into your new collection. Now if you click on your new collection header bar, you’ll see all your selected documents. Shift click on the first and last in the list, toggle cmd-1 and you’ve got your virtual document again.
b) Printing them all out as a single document.
This is done from the Compilation dialogue. (File > Compile. Choose All Options, then Contents and you can tick whichever files you want to include.
c) Document Notes – with a single document selected, View > Inspect > Notes will give you the Notes panel. With multiple documents selected, View > Inspect > Notes will give you the Project Notes.
However, it seems to me that there’s something about your expectations that we’re not understanding here. It may just be a question of vocabulary, because it’s perfectly normal to have several levels within a project, so that shouldn’t be a problem.
Perhaps if you could explain a little more about your setup? For example, you keep mentioning ‘Files’ rather than documents - -what’s in these files? Are they pure text documents, or something else like pdfs / mp3s etc? Where are they in the Binder – under the first folder in the Binder (Draft or Manuscript usually) or somewhere else? What’s the ultimate goal of the project (a novel, a series of novel, a technical manual, a screenplay, a TV series etc)? All of these can easily be implemented within Scrivener, and it may help us to help you better if we could picture what you’re trying to do.
Finally it doesn’t look like you’ve gone through the Interactive Tutorial yet as Keith suggested. You really should. It will take less than an hour and it will save you a lot of frustration. It will take you through the basic concepts in enough detail so that if nothing else, we’ll be using the same vocabulary and we may be able to help better if there any problems remaining.