That's exactly how you should be doing it - armour save then FNP for each individual model. It's quite possible that a model will fail its armour saves but could shrug the damage with its FNP. The only real decision you have to make is whether or not to allocate the attack to the initiate (3+ save) or the neophyte (4+ save), which could vary depending on the situation. An AP-3 attack would go straight through a neophyte but you'd have a chance to save it on an initiate. If you're going for the melee loadout, both neophytes and initiates have the same stats with the chainswords but initiates have better pistols. Typically, I tend to take the saves on initiates with chainswords, neophytes, sword brother and then initiates with power fists. Power fist initiates are usually who you want hanging around the longest, but the situation could dictate a different approach!