What Aussiegiant said, plus:
Look at the city screen, there are bars full of icons showing reasons for happiness and unhappiness for the different classes of the conquered city's population. Examining these should give you an idea what's causing unhappiness and thus how to mitigate it. However, immediately after conquering a city the biggest cause of unhappiness tends to be 'occupied by a foreign power', there isnt much you can do about this except wait - it gradually disappears over half a dozen turns or so.
One important thing to do is to make sure you repair any buildings immediately after conquering - i've found that leaving cities 'smoking' tends to cause a lot of unrest. This can be quite expensive for the big multiple build slot cities so make sure you have plenty of cash ready if youre attacking one of those.
Another trick is to send your preachers in *before* youre going to invade, so that youve already converted the majority of the populace by the time youre in charge. Remember to destroy any religious buildings that arent of your religion immediately after conquering, and replace them with ones of your own religion (besides the conversion rate increase it gives a happiness boost to members of that religion).
Sometimes, when i'm organised enough, i have a 'pacification squad' consisting of half a dozen dragoons which follows 1 turn behind the actual attacking army. These guys can move in to replace your main army after a conquest, which frees it up immediately for more delicious, tasty slaughter. They can sit on the population until things quieten down, then you can locally recruit some bog standard garrison troops and your dragoons can move on to the next hotspot.
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