Ok, so I went back and spent some time playing around with arena settings, and figured out how to save my settings.
I have to go into arena tables, and save the settings to host. And then when I start a new arena, I have to go into Arena Tables, and manually upload the settings file.
On the screen where you set the arena flags, there is a Save button, and a Load button, among others. But they don't save or load the settings. I have to go to the Arena Tables screen, and then I can save and load the setting from there.
What was confusing me, was at the start screen when you first start an arena, there is a field where you can set the configuration file for the arena. But it doesn't work. I use the drop down list to select the configuration file, and none of the settings take effect in the arena. Once the arena is started, I have to go to the Arena Tables screen, and upload the file. Only then do the settings take effect.