V&Vs only affect the stats of a general and his unit (apart from those applicable to governors affecting provincial happiness etc). Valour or morale affects the unit as a whole, loyalty command, piety dread and acumen only affect the general himself, but of course as command affects all of the units in his stack this affects all of the other units valour (only). So you can think of vices or virtues affecting command as the only ones that will affect the army as a whole.
-Edit: I'm slipping a bit. The vices that incur morale penalties such as "doubtful courage" also affect the whole army stack. Beware of these as they can ruin a good general. You may be in a battle and wondering why your men are running away despite the generals stars, check his V&Vs.
Those vices and virtues relating to valour do only affect that general's unit though and not the whole army.
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