There is even a button called "Bake Selected" ( the little oven bakes the selected vertices ). In the same button row are tools to completly exclude vertices from specific bones Another thing that might help are named selections: select your vertices and type a name in the Named Selection field.
If you take a look at the reference option box there are three options: 1st to give the file name, 2nd to give another custom name and 3rd not to rename it. The recommended workflow is really to give the file name, giving a prefix is necessary to avoid repeated nodes in the scene and to maintain consistency.