I have two GTX 970´s one 04G-P4-1970-KR reference and one 04G-P4-1972-KR superclocked. I am new to sli and would like to know the best config using EVGA Precision X16.
Should i
a) Sync or Link both cards even though they are different speeds (what is the difference between Link and Sync?).
b) Should i unsync them and overclock the reference card to the same speed as the Superclock?
 
also 
 
which card would be better as GPU1?
why does the reference card run hotter?
 
Many Thanks

a. Link/Sync are the same thing.
b. Only if you want the slower card to run at superclocked speeds. 
 
1. They will both work the same as GPU #1.
2. Both of your cards are based on nvidia reference design. No two cards are exactly the same, one card may be using a bit more voltage than the other card which is causing it to run a bit hotter.