Okay... First off, please do not reveal to me further on in either of the two story lines I will mention as I have not done them yet.

Now my question and situation: On my character I have chosen to do the dark brotherhood quest line before doing the 'war' where i pick the stormcloaks or the imperials and take part in that big civil war thing.

But I just got to the point in the dark brotherhood where they want me to assassinate the emperor... If i go through with this, will this conflict with my ability to go through the war later.. doesn't the emperor control the imperials?

No, it doesn't really change anything.

As far as I'm aware it shouldn't ruin anything for you. Tullius is the one in command of the Legion in Skyrim, and he'll probably do his thing regardless of who's his superior.

Yes, an emperor usually leads and empire, that's why they call it an empire

I can't speak authorativly on this, but if you're doing your job right as an assassin, they won't know you were responsible for his demise (Unless you get caught...) and thus no repercussions for you will arise in persuing the imperial side of the civil war. It's unlikely his death will affect the civil war story arc as General Tulius is in charge of the imperial forces, and the loss of their current leader won't really change anything on the battlefield.

This is just guesswork of course...

Nah. As military governor, General Tullias commands the Imperial forces in Skyrim. I don't think anyone else immediately knows what's happened.

Okays, My worry was the Emporer himself was involved in the civil war story line, and eliminating him would cause me not to be able to do that later, but 3 folks here have said General Tullias leads the military so that should work.

And yes, my character's now 81 and very adept at sneaking.. and has the nightengale bonus for temporary invisibility, and all the perks under marksman/archery, so she's never, ever seen when she assassinates someone..