'audio instrument' vs. 'midi instrument'
Well let's start there. An "Audio Instrument" is a class of an audio object, and it's displayed in the environment as a regular audio channel, with a fader, input and output, inserts etc. It lets you insert an instrument plugin in it's input, and receives MIDI data which plays the loaded instrument plugin, the audio of which is played to whatever output is selected.
A MIDI instrument is simply an environment object that takes incoming MIDI data (optionally processes it) and sends it on either to it's cable output, or to a MIDI port.
So if you have an external synth (say, Virus) connected on MIDI Port 1, on MIDI channel one, you'd create an instrument object called Virus, and specify Port 1, Channel 1.
Now with that object selected on an arrange track, the MIDI in your regions will be sent through it, and out to MIDI Port 1 on channel 1, and your Virus would play the notes.
Finding patch lists isn't a problem, because I have those
Ok.
But I can't seem to successfully copy and paste them into the banks.
I goto bank 14 and select "paste all names" (which I have copied
from the patch list in my word processor) but the names get
pasted to bank 6 instead!
Er, not sure what's going on there, I've never had a problem pasting in names - it's difficult to say without seeing what you are doing. You can always copy banks of names between banks anyway.
Another problem is that I've got four new expansion boards
I need to initialize and I've already filled 14 of the 15 banks
available in my JV-2080 multi-instrument.
Yes, that's a little more tricky and has been a limitation of Logic for some time. Thre are ways around it that involve some environment work, but if you're a newbie at that it might be tricky...