@Blinx123: If you're using the latest version of Chrome's Ripple Emulator (0.9.13), there is a Build panel on the right-hand side of the screen. Within the Build panel is a Settings dialog.
You will need to populate that dialog with the path to your SDK, the path to your folder, your project name and build ID, and your code signing information.
Once populated, you can close the dialog and Start Services which will launch a command prompt. You can then hit Package and Sign to create the BAR file.
From the sounds of it, you're having some core functionality issues within Ripple though. Would you be able to fire me some screenshots of what you're seeing to email@example.com and I'll do my best to provide some insight?