You train charms by training the ability, basically. There's no real distinction between the two.
Also, on a more general note, I made a tweak to the character sheet and switched one of Ignatius' favoured abilities from Linguistics to Resistance. This is mostly because I went and looked at my plans thus far and realized that the former would only very rarely see use - 40k doesn't have a great many situations where you can hand-write a letter to someone but cannot call them on the vox or make the trip in person. It does, however, feature a great many situations where being able to deflect lasgun rounds from your abdominal muscles is a useful ability to possess.