I'm having the same problem. Searched Stardock's website, forum, and wiki for hours, but no description of how the sector numbering on the grid works in Galactic Civilizations II (galciv2). I finally figured it out, though. I remembered that if I set a rally point and then looked at the details of that rally point, that it gave me its coordinate. After placing rally points all over the board, I have finally discerned how the coordinate system works.
On the mini-map the galaxy is shown as a diamond shaped grid. The bottommost point on the grid (south) is coordinate 0,0. As you move up-and-right (northeast) from there, the first number in the coordinate increases (like 37,0). As you move up-and-left (northwest) the second number in the coordinate increases (like 0,56).
So, sector 1,3 is extremely close to the bottom of the map. I suggest using the rally point method to find exactly where you are headed.
As for receiving instructions on how to get there undetected...I'm 20 turns in and have not received any. I've talked to the Korx but all they want to do is trade. I've revisited the Campaign Manager's Victory conditions, but there is no new information there. I'm not even sure what I'm supposed to take there (I'm guessing its this badass ship called "Crimson Blade of Kas' Prinra".
If anyone has more information about how to get these mythical "instructions" please comment here.
Edit: Looks like I was wrong (partly) on the whole coordinate thing. The rally point coordinate is actually a parsec coordinate, I believe, not a sector coordinate. I had sent many ships to parsec 1,3 but didn't win the game. After looking at other postings, I was educated on where to find my current sector. It is right at the top of the screen in the middle. Duh! 
After going to sector 01-03, my game ended. The sectors are numbered in the same fashion as the parsecs...with 00-00 being at the bottom point on the mini-map. Sectors are deliniated by green grid lines on the map. So 01-03 is the second one to the northeast, and the fourth one to the northwest.
BTW, I won with only a ship with engines and life support on it. I didn't have to get the "Crimson Blade of Kas' Prinra" to that sector (It actually got destroyed earlier in the game).