Each folder in the Plugins SDK contains scripts for creating new plugins for that type. New plugins are placed in their own subdirectory of the appropriate plugin directory. For instance, a new portlet called "greeting-portlet" would reside in liferay-plugins-sdk-6/portlets/greeting-portlet.
The Plugins SDK can house all of your plugin projects enterprise-wide, or you can have separate Plugins SDK projects for each plugin. For example, if you have an internal Intranet using Liferay with some custom portlets, you could keep those portlets and themes in their own Plugins SDK project in your source code repository. If you also have an external instance of Liferay for your public Internet web site, you could have a separate Plugins SDK with those projects as well. Or you could further separate your projects by having a different Plugins SDK project for each portlet or theme project.
It is also possible to use use the Plugins SDK as a simple cross-platform project generator. You can create a plugin project using the Plugins SDK and then copy the resulting project folder to your IDE of choice. This method requires some manual modification of the ant scripts, but it makes it possible to conform to the strict standards some organizations have for their Java projects.