Thanks! I had considered just editing one of the already existing start up scripts, but I didn’t know which one to use.
In the end, I decided to use a different method of running my script. I learned that I could have the script called whenever I plugged in my controller by making a rule in the /etc/udev/rule.d folder. See
https://raopinion.wordpress.com/2012/01/27/mayflash-n64-controller-adapter/
I was pretty disappointed though. I spent hours configuring my controller setup only to realize that n64 emulation is pretty bad. Most games run fast with the rice plugin, but for whatever reason, the menu textures are shot. I wonder if any future updates will correct these issues…