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Like BlaxkDiamond, I do a combo of both

Because my main focus is on superior breeding quality, I always run my foals through SBA. Those who survive the cut then are compared to sire/dam. If they are only as good as or worse, they are spelded.

If I end up with more than 2-3 colts that make it through that, I start comparing their genetics and bone weight as my 2ndary goal is super duper heavy bone. If the colt is homozygous for most of the genes including those I can't adjust in the GMT lab AND their bone is super nice, that's generally the winner. Fillies, I generally keep as long as they are superior to their dam and pass SBA. I might spot check a few here and there by comparing to my benchmark mare for that particular generation but I find that because of such a strict culling regimen, my mares generally are all same quality.

I don't bootstrap on this account yet but I only use the comparison test on the fillies. Superior fillies are only kept. I do keep a few fillies that test as good as their dam IF they are testing as good as my benchmark mare. Colts are run through BA and that's how I determine the quality of my bootstrap herds. If I start getting more and more colts that pass BA, I'll start comparing to their sire and if I start getting as good as sire colts, I know I need to upgrade my BS stud either by breeding a superior son or taking one of his AGA sons (if I love everything else about that colt) and boosting.