We get this question fairly often but it's not an easy one to answer. I, for one, dump all of my points into the SS specialty (+%), even early on in a reincarnation. The strength added by our camps is also used in calculating the +% modifier (I believe) so that's why I always prefer specialty stats!
But until your character reaches 200 in a main stat, putting the training point into the specialty won't be better than just putting it into the stat directly--and putting it into the stat will make your SS better at all 3 actions of that stat, not just one. I know some Officers prefer it this way, so it's all apples and oranges, really!
What it really comes down to is whether or not you'd like a SS that excels in one substat, or a SS that is moderately good at every action of a main stat. What do you think, how should you level your SS?