Depends what you mean. When you have a local mpk-file; right-click on the folder / module where you want to place this and select "import document" and in case of a module; right-click on the project where you want to place this and select "import document".
When you update a module from the appstore, till someone has a better process, delete the existing module and relevant folders in the "javasource" folder before you import. Than make the changes again. Because of this process of updating I always make sure I use the function of modules from the appstore by triggering them from another (custom) module and leave the module form the appstore intact.