First go into the actual app... (Option click or right click), "show package contents") and then content/resources/apophysis and deleting the "Apophysis.exe" file And replacing it with "Apophysis mods Jk" found here. [link] When you replace it, you have to right click (or Option Click) the file and change "Apophysis209 JK.exe" to just read "Apophysis.exe" or the script found in the app simply won't be able to find and launch it.

Then most importantly, go to (your home folder)/Library/Application Support and deleting the ApoMAc folder in there! You must do that or it will just keep opening up the version you deleted.

Then because Mac indexes everything, you have to empty the trash. After that, launch ApoMac. Once it's launched click on options, then from the drop down options again. When the options box comes up you will see a tab that says "Plugins", click on it and browse location by clicking on the folder icon in that tab.

Now once you locate the Plugins folder, (where ever you saved the plugins at), open it and you MUST click on one of the action plugins. Not sure why, but it seems to be the only way it works. Then click open, and click OK.

The plugins should now be loaded. And if not close out ApoMac and re-launch it. You will get a warning mess. every time saying that the plugin you selected could not be found. That's alright, just click OK. It appears to be a glitch, but they will be there.

If anyone gets confused, then leave me a comment.
If I get more than five requests, I will post a quick Video
walking you through the steps.