Its the best way to equip soul from the owner to him? Example: Bort´s soul is worth more on himself than on any other fam.
I have found that if you plan on using that same guy after you evolve them, its a good idea to use their own soul as it already has the better stats for them that they need.
This is only really possible on commanders you can actually evolve with minimal effort. Otherwise you are left trying to put that soul on someone else.
If you have no intentions of using the next form of the commander you evolve then try to find someone to use it on your main squad or pvp squad.