Unpack the archive and go to the directory where you put the files and type:
java -jar bin/Browser.jar
If you run Windows and have Java properly installed, double clicking on Browser.jar may also work.
As a next step, you have to load a data file. Selcet the menu item File and Open and move to the examples directory of your yWays installation which contains two metabolic pathways. Select one of the example files and click open. This will load the corresponding file into the browser. On the left side of the browser window, you will see all compounds of the metabolic pathway in a list.
The next step is to calculate a layout for the pathway. Select Global Layout in the Layout menu and choose an automatic layout algorithm. For metabolic pathways the hierarchic automatic layout algorithm fits best.
To change the diagram you can use the Options menu. Note that it is often required to calculate a new layout when you changed an option.