no need to put it on both maces. I'm an archer mage, so I have it on one of my bows. For low level stuff it is a one shot kill and auto capture. For high level stuff, I can either cast the spell which lasts 60 seconds, or damage the enemy almost to death and then switch to my soul capture bow to finish him off and get the soul.
Others more versed in melee combat in this game may have different opinions, but for you this is what I'd do. Put soul capture on a light bow. That way you can shoot deer, foxes, and other small game with one shot kills and easily fill petty/lesser soul gems. You need LOTS of those to grind through raising your enchanting level.
Personally I think you'd be better off putting damage enchantments on both maces and then switching to your soul capture bow to deal the death blow if you want the soul. Either that or buy a soul capture spell and cast that on the enemy. Seems like having the soul capture on one of your maces would lead to a couple things - using up charges quickly on the mace, and if you have just the 1 second soul capture enchantment on the mace, possibly dealing the death blow with the other mace and not getting the soul.
Maybe I over thought that part.