It depends and could be hard to change if you already reached a specific point of bad reputation. If you need to raise a specific town's reputation, you need to do normal quests from that town, as well as town quests from the town hall. Town hall quests give only +1 to reputation.
But if you already have too much bad reputation with groups like e.g. the varannari, then i think its too late for changing it.
I did a quest "safe travels" I think and robbed him at the end of the quest. Then all of a sudden NPCs started attacking me. Well, I couldn't have that, so I started smashing them. Next thing I know I'm at -100 reputation.
Just reload from one of your saves. If you murder people, yeah guards will kill you and I think the dialogue gives a warning about it. But in theory it will only happen with one kingdom, you will be able to do everything in other kingdoms. And I will add a way to fix your rep. with Mercia but I can't spoil