I'm not sure to what exactly you are referring, so I'll tackle input and output.
By default, all available MIDI interfaces come into Logic at the Physical Input object
in the environment (Click & Ports layer). The sum of all those will be fed into the
sequencer, so if it's a valid input that OSX sees, any MIDI coming down it will be
squirted into Logic.
You can take specific ports from the Physical Input
object, rather than the "Sum" output, and do things with them individually if you want.
Now, Output is a different thing. You set Logic up to talk to your Instruments, so
you don't have to remember what port and channel they are on.
To send MIDI to
your Nord Rack for example, in the environment, go New -> Instrument. Call it Nord Rack,
and specify in the parameters than it's on MOTU Port 3, channel 6 (or whatever).
Now, when you want to play the Nord, or sequence it, simply select the "Nord Lead"
instrument on a track, and all MIDI will get routed there.
Does that answer you