Assuming skills that use the standard progression:
The bonus/penalty for category is added to the bonus/penalty for the skill.
0 ranks in each gives a base of -30. 1 rank in the category gives a base in all the skills of -13 (+2 for the category, -15 for the skill).
0 ranks in RM2 gave a -25 modifier. RMSS gives a higher penalty for no ranks at all, but if you've developed the category, you'll be better off with skills you haven't developed than you would be with RM2 (unless using one of the RM2 similar skill optional rules, which is what the category system is designed to replace).