Hello,
Probably you need to first
mv ~/on-startup/load_default_patch_disabled ~/on-startup/load_default_patch
so that the script gets called when it boots.
Then, as far as I recall, that loads the patch ~/on-startup/default-patch.pd (or something like that). You can check by running the command
cat ~/on-startup/load_default_patch
(after you have renamed it :) to check what it is calling.
So, at this point, you can simply replace the default patch, but make sure if it needs any abstractions for that it can find them. (i.e. put them also in ~/on-startup/).
From the terminal, you can also check if it's working by first quitting all instances of pd and then typing
~/on-startup/load_default_patch
Best!
—Edgar