The saddle CAN make a huge difference. Keeping it within a brand -- the Brooks Swallow/Swift is torture on my 6,000-miles-per-year backside. The Brooks Team Pro (just 5 mm wider) defines comfort for me.
Another issue is distance. Fizik's Arione is great for me for distances of 50 miles and less. Beyond that, and I've ridden the Arione many times, but my backside didn't enjoy the last miles very much.
First, make sure your saddle fits you (not your riding buddies or a participant on the BF). Once you've done that, I'm not sure the shorts matter all that much, so long as they are quality shorts and don't have a misplaced seam.