If you've only added the framework to the WO Frameworks section of your build path, it will be using
/Library/Frameworks/YourFramework.framework. If you want to use the Eclipse project version of your framework instead, you will also need to add it to the Projects tab of the Build Path (see Project - Properties).
At this point, you will have both versions of the framework in your classpath. So you will need to specify which one is the one that has precedence. If you go to the Order/Export tab of build path, you will want to move the Project reference above the WO Frameworks reference so that your project one "wins".
Note that you should have both references in your build path, because the "WO Frameworks" one is used when you deploy.