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The first step of programming WOLips is Building WOLips. Once WOLips is properly built, then you're off to development. Development inside of Eclipse will give you the most power, but to take advantage of it will require a few additional steps when you want to do a full build again.
The main problem is that the PDE build of WOLips gives you all the plugins, but to deploy you need to build the "woproject" top-level project from Subversions, which CONTAINS the same plugins that you have checked-out as individual projects. What that means is that you will be mainly working in the plugin projects, but your "woproject" project will become out of sync as a result. When it comes time to deploy again, you will need to either commit your changes and update your "woproject" project to get those changes; or, you will need to manually copy your changes over to the woproject project.
Once your changes are updated in "woproject", you can follow the build instructions in the "Checking out and Building inside of Eclipse for Deployment" section of Building WOLips.
One problem you might run into is that your build number doesn't increment and you cannot update your plugins from the update site if that happens (because the versions are the same). The quick fix for this is to manually change the value in build.version inside of the woproject project.