Standard painter's advice follows...
If the base is metalic or any kind of 3-part (candy, etc) do the whole piece. There's no way to get a seamless blend. If it's a solid color AND YOU HAVE AN EXACT MATCH PAINT, you can blend the base color but you really want to clear the entire fairing. Urethane clears do not "blend", they always leave a line where the new clear overlaps (exception noted below).
By "exact match" I mean YOU painted the fairing the first time and have leftover paint from that batch. Or, you know what brand and paint code was used and you can duplicate it exactly. Anything less than that and you're kidding yourself. Trust me on that. A fairing only needs 1/2 pint of paint to do the whole thing, I wouldn't risk a mismatch for that.
You need to sand the blended area to whatever scratch the base needs for adhesion, typically 800 or 600. Make sure you check for a real matte finish with no scratches that the new clear won't hide.
On blending clear:
I use Glasurit 155 clear ($$), one of the best in the world. Glasurit sells something called "blending clear" that's essentially a very hot reducer. After clearing the repair area with 155 you spray a VERY light mist of this stuff around the outer edge of the new clear and it "melts" the new clear into the fine scratch around it. It's the only way I've been able to clear a blended area without it showing.
Questions?