Pics would be helpful so we could see where the scratch is. I'd say yes to gluing down the patch first and no to making holes at the end of the scratch snce the patch with be sewn on and remove most of the stress from the scratch and carry the load. I certainly would be concerned about stretching and shrinking with dissimilar leathers but as long as the stiffer of the two is the patch I think you'd be ok.
Also, unless there is a traumatic memory of the event, it may be kinda cool just to do like a baseball stich across the scratch and leave it visible. Call it "character mark no.1"?