Thank you for using eclihx ide)
The haXe Build Paths panel for the project is really intentionally empty. I had some plans to implement features of configuring the project skeleton but I think they have less priority comparing to the other features in the project. So I decided to leave a basic structure for the project for the first time.
Despite this I've probably found a solution that could be useful in your situation.
1. Create a haxe project and call context menu on the src folder
2. Proceed to New->Other->General->Folder
3. On the "New folder" dialog click the Advanced button
4. Select "Link to alternate location" and add your external source folder
After that you should be able to see your files under created project. The content assist feature should also work, but there will be a problem with navigating to the error places from "Problem View". You can post this defect to issue tracker. Although it will be priority enough I would like advise to you to rearrange your source folders to the single one :)
Best regards,
Nikolay Krasko.