Minecraft Essentials question?

How do I add a Pex Permission to: / money and in Plot Square e.g.: / p h

You have to change the source code of the two plugins. If you have downloaded the plugins, you can e.g. Decompile them with JD-GUI to get the source codes. You can then save this source code as a zip file and open it with an IDE of your choice. Now of course you have to add Pex and you can build in your permission query.