Do I need a separate proficiency to use a weapon's secondary attack, or do I only need proficiency in the main weapon? For example, if I have a kombi-shoota which is a shoota with a one-shot rokkit launcha, can I fire the rokkit launcha without penalty if I only have proficiency in shootas, not rokkit launchas? Does burna proficiency cover the secondary usage as a burning blade? Does shotgun proficiency cover the shotgun's melee attachment? etc.

If you have a weapon that shoot SP rounds you need the Basic Weapons (SP) Talent. If you have a weapon that shoots SP rounds and a combi weapon on the same frame that shoots Bolt rounds, you need Basic Weapons (Bolt) Talent. If it has a Power weapon on it, you need Melee Weapons (Power) Talent or Simple or Chain or whatever the melee attachemnt is. Just buy the Basic Weapons (Universal) and Melee Weapons (Universal, Primitive) and Pistol Weapons (Universal) and you'll be fine, Universal coves ALL weapons except Primitive, but if your useing Primitive ranged weapons in Rogue Trader your dead anyway, Armor AP doubles against Primitve Weapons, youd never hurt anyone. And if your useing a Primitive Melee Weapon, youd better put Mono-upgrade on it so it losses the Prmitive Quality, even though it still falls under the Primitive Weapon Proficieacy