I killed 3 imperials ( Since I am a stormcloak I kill them when they are on the roads )

And I have a bounty. If I pay it off will it be as if it never happened? Like will people start to hate me and not like me all will I be able to continue with people liking me?

There are hidden disposition bars. So some people may not like you, cutting off follower opportunities, and maybe raising prices a bit.. nothing too bad though.
But that can be easily fixed by doing some misc quests or saving the town from a dragon.

There is no morality system in TES games.

no.