Lots of reading to do! x_x
Here are some useful forums with a lot of info, might have to dig and search for some answers though.
http://eccs.hybridka.com/
http://www.ka-t.org/forums/viewforum.php?f=36
It's common for people to get an adapter that allows the S13 ECU to connect to the S14 harness, and you can tune it like that from there.
If you want to tune it yourself, I recommend going with a Calum or Nistune daughterboard, as they allow you to change the tune in realtime.
If you have a regular mail order daughterboard with a tune on there, you'll have to take off the EEPROM chip everytime you want to upload a new tune to it.