I'm not really sure about wire colors to test it. Does your sub work at all right now? I think it can be wired to work even with an aftermarket HU. Is your sub in the console or the rear cargo area?
My sub and amp is under the console. But mine is an 04 and an XL. So I'm not sure if yours is the same.
I think you need to search the 00-06 audio forum and/or post a question to find out if I'm crazy or not about being able to run the Bose amp off of a non OEM radio.
Like I said I have a working OEM radio that I took out cause my amp died. I just put in an aftermarket HU and an amp to run my Bose sub until I have time to redo my system.
So find out how to test your Bose amp and just PM me if you need my radio. I will get a pic of it sometime fairly soon. ( having a little family issues at the moment)