You don't actually have too; that "perfect pair" method is honestly a hold over from the pre-incubator days, when you had to mass hatch with AC units. It made spotting new mutant babies easier when hatching 50 at once.

With an incubator though, you can easily skip it and go straight to mutating. Simply find the creatures that tamed out with the best of the stats you want to mutate, like health & melee for rexes. If male, great, if female, mate with random male until you have male with that stat.

Then mate your best health male with a bunch of females; about half the eggs will have his higher level, say 40. Name him 40 health. Then keep mating him and checking eggs until you get a 42 health egg; name that one 42 health. If male he becomes the new health breeder, if female mate with non-mutated male until you have a male 42 health. Then go for 44 health, and so on. Repeat this process for melee, and then at the end combine the lines. By naming breeder males their key stat, it is stupid easy to spot desired mutations. You will end up with a line of mutated males per stat; always use non-mutated females for the breeders. With this method you can use any random females you have around, as long as they are non-mutated. Only mate mutated with mutated when you combine the lines (i.e. have your final health male mate with female until you get female with final health stat, and mate her with final melee male until you have male & female with both stats).