I'm trying to get accustomed to x3, coming from sonar 5, and I can't seem to use Bank 0 Instrument 0 as an instrument number.   Is there a setting somewhere to indicate 0 or 1 as lowest number?    

It could be a problem because I'm using instrument definitions imported from sonar 5...
 

Myself I enter the bank and instrument in the track inspector view. The event list is kinda DOS old school and not really a place to do much other than look see whats going on. 
And Bank 0 instrument 0 is actually nothing, so you just get piano. You get the same piano using all other banks patch 1. 

I assume you are referring to an external synth. You are correct in thinking that the bank and patch information is stored in the instrument file. You can edit that to set it up to match the synth. Bank changes require a Bank Change number which you'll either find in the synths manual or at least the info to calculate it.
 
If you need help with that post up.