If the unit being attacked contains models with different Armour Saves, the same procedure is used as for shooting at mixed armour units. So, the opposing player rolls to hit and to wound for whichever unit they are attacking with as normal. However, when the defending player makes Armour Saves, they use the best saves as long as the models wearing that type of armour are in the majority (ie, they outnumber models with worse Saves in the unit). Any casualties which are removed after saving throws have been taken must come from amongst the most heavily armoured models first (ie, the ones with the best Armour Saves take the hits).
If heavier armoured models are in the minority, use the worst Armour Saves and take the casualties from the lightly armoured models first. If there are more hits than the majority type, distribute them out so that all go on the majority type before hitting minority models, in each case, the differently armoured models get to use their own Armour Saves if they are hit. If there is no Save type in the majority, the owning player gets to decide which group gets hit first.
Example: A squad of Black Templars Space Marines includes four Initiates (Sv3+) and six Neophytes (Sv4+) is inside the enemy's 2" Danger Zone. The squad suffers eight wounds in close combat. There are six models in the unit with a Save of 4+, so six Armour Save rolls are attempted - four fail and four of the Neophytes are removed as casualties, the remaining two hits spill over onto the Initiates and are saved using their 3+ Armour Save. If a unit has Invulnerable Saves also, it must be taken on the worst of the invulnerable saves first.