If you set the MAYA_PLUG_IN_PATH in your Maya.env file as described in Setting up your build environment, plug-ins in the top-level of that directory will be loaded into Maya automatically. However, plug-ins that are not in that directory's top-level will need to be loaded manually.
If your plug-in uses dynamic libraries, it must be unloaded before it is recompiled otherwise Maya will crash. It is good practice to always unload a plug-in before rebuilding it.