ok, so currently you have a headless OSX box, i'm guessing this is a Mac Mini from the sound of it?
you want to have pure data start right when you start it up? or are you going to be using some sort of remote login (do macs have SSH?? OSX is basically Unix these days so i would think they do)
basically the command line arguments are passed to pure data when you start it up
so for example, lets say you;re starting it from a short cut. the shortcut has the path to the PD executable. if edited the short cut so it was
"/path/to/folder/pd.exe -midiindev 1 -midioutdev 2"
then pure data wouldstart up and get the arguments passed to it and then know that its using midi device 1 for input and midi device 2 for output.
o lets say you want to start up PD without the GUI, with midi device 1 as input, midi device 2 as output and you want the patch awsumsounds.pd to start up, your command line would be
"/path/to/folder/pd.exe -nogui -midiindev 1 -midioutdev 2 -open /path/to/awsumsounds.pd"
apologies if you already get this, wasnt sure how basic to start so i figured the beginning is best heh.
if you wanted pure data to start automatically when you turn the machine on then youd have to put a shortcut in whatever mac uses to run things at startup.
alternativly you could start the machine up, ssh into it from another machine and then start pure data yourself using the command line above, however you might need to play tricks to get it to carry on going after you log out.
hope thats all helpful, i'm afraid that i dont know about some of the more mac specific stuff