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My suggestion would be to simply add a +10% to the new skill; it was an important part of their training at both schools, and they learned something new from the Secondary school (since there's always something new to learn, especially from different teachers).

And how many people are choosing martial arts for the skills?

The way I handle skill overlap is to add a level's worth of % or bonuses to the skill that has the greater bonus or level progression.

Given that there are a lot of skill programs with auto-pistol in them in NSS. If you had three programs with that skill, the char would start out with the A-Pistol at L3.

If you go with what mark suggested with what is for most skills a 2 level bonus, the above char would start with the wp AP at L6.

I use this mostly when combining the sub skills in Gym and Acro.