The first thing you must consider in choosing the pair is what you want to get as a spawn.  For example, if you choose to get a white opaque spawn you (most of the time) would obtain a white opaque pair (in some cases you can cross a blue or turqoise to a white and get some white...) to breed.  If you want to get certain types of  finnage, you would choose by looking at the phenotype of the female betta (in other words, the female is responsible for the spawn's finnage quality and the male is responsible more for the color; this is not 100% true, but is close enough to hypothesize the outcome).  Anyway, set your goals for breeding so that you can get the bettas you want. (fig. 1)

I prefer to start off with other peoples lines (not exactly their "lines" but more like their bettas--for color and finnage; like buying a solid color or known pattern from someone) just because it's a lot easier and the spawns come out just right.  I do, however, have my own personal goal as a breeder and that would be to create a extreme piebald red BF betta, where the piebald recedes to the beginning of the dorsal fin (fig. 2).  I would call this pattern the Hi-no-Maru™ (Japanese term meaning "circle of the sun"--literally, "the rising sun"; to represent the Japanese flag). 

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probably 10% of fry being true HMs and pure blue (or green) color w/out any red wash.

(Fig. 1)

(Fig. 2)