First off, I'll assume that you have downloaded the CS+ port of Cave Story 2. Extract the contents from the zip file into some folder.
To use Plus Porter, you first want to go to File -> Open CS+ Directory, and browse to your Cave Story+ installation. To apply a port that has already been made, go to "File" -> "Open port...", browse to the folder of the port you wish to open, and click "Open." After the port has been loaded, go to "File" -> "Apply port", and a window will open up listing all mods currently installed in that game of CS+, and the order in which they'll be listed in the challenge menu (with the one at the top appearing on the main menu). You are able to arrange the mods in whatever order you want the challenge menu to list them, and then click the "Apply port!" button to apply the port to your Cave Story+ installation. Exit out of plus porter, and you'll now be able to experience the mod in Cave Story+.
Sorry about the somewhat unintuitive way that opening and installing a port works. If I were to make Plus Porter today, there are several things I would do differently.