You need to reduce popular discontent in those territories. You can do this a few ways (and it's best to use combinations of them). If the regions have schools, get rid of them. Build Entertainment centers and churches instead. The entertainment centers will help counter discontent and churches will convert the population to your religion which will also reduce unrest. Garrison the capital of the region with troops. The dragoons get a bonus for garrisoning (but there are a couple countries that don't get them; I think Russia does, though).
If the populace does rebel kill the rebels as fast as possible (they grow in strength every turn). Killing the rebels will also reduce unrest (the dead can't cause trouble).
Check your ministers for any that are causing minuses to aristocracy/lower classes happiness. Some of them can really make a difference (especially it seems when they are in the Justice Minister slot). Sometimes it takes shuffling them around or booting the bad ones. I really haven't come up with a hard and fast rule on who to keep or nnot. I often save the game immediately before trying to boot anyone to see what effect it will have.
Unrest usually doesn't come down fast. It can take time for it to drop and with that there might be a lot of rebellions in that region. At times it isn't unusual for me to take 9 or more turns to finally subjugate a region so I don't have to leave a huge garrison there.
Also, some levels of industrial buildings will contribute as well. Also some tech advances cause unrest to increase.
I hope that helps a bit.
Life was much easier before I developed a sense of ethics.[This message has been edited by Warguppy (edited 05-09-2012 @ 12:23 PM).]