To date, I have been to Whiterun, Winterhold, Solitude, and Riften. Within the Main Quest, I have been to Winterhold, and have to go north exploring. I have not started the Civil War quests at all, though I do plan to do so next to get that going. My question is this, based off what I have done so far, or want to do with the Civil War quest, will I eventually see all the cities, or should I just walk through the main gates and start introducing myself to everyone? (Little as possible with the spoilers.) Thanks!!

Without giving away to many details there is only 4 cities the Civil War will require you to go to.

Whiterun (Stormcloak / Imperial side)

Riften (Imperial side only)

Markarth (Stormcloak side only)

Windhelm (Imperial side / Stormcloak side)

Solitude (Stormcloak side / Imperial side)

So say you want to join the Stormcloaks. Windhelm is the first city. Eventually you'll be sent to Whiterun, the second city. You'll be sent to Markarth when taking the Reach for a little blackmailing. Third city. Finally you'll take the fight to Solitude. Fourth city.

So as far as I see it you might as well visit all the towns and not just stand around at the front gate

Morthal is the one hold I have yet to find my character "directed to" in some way. I could be wrong as I have not done everything in the game, but it seems like if I want to go there, there is no "underlying reason" to do so, other than "Look! There's Morthal!"

The Imperial side of the CW also sends you to Dawnstar. I'm sure that the SC side has a similar quest, but I can't remember which city that involved (I'm thinking Morthal or Falkreath).

Edit: Looked it up, the SC side sends you to Morthal.

I've encountered one quest that sends me to Morthal, from the

Edit: Also the SC CW questline.

Are those random/radiant quests? I have been sent there with those.

Whiterun, you are directed to.

Winterhold, too, for the MQ or if you want to be a Mage.

Riften is in your path through the MQ and also if you wish to be a Thief.

Markarth has the "Drinking with Sam" quest that literally throws you into the midst of the city.

Solitude is in your path if you go through the DB questline or the Civil War - Imperial side.

Falkreath is thrust upon you when you reach level 8 or 10 with Hearthfires installed.

Dawnstar, you get a Museum Pamphlet at level 15.

I am struggling to find a "directed quest" for Windhelm, other than the Civil War - Stormcloak side.

Morthal, I can not recall a "directed quest" to go there, except the quest you mentioned, so I am corrected

Don't forget

Sent to Morthal via DB http://www.uesp.net/wiki/Skyrim:Kill_Lurbuk.

I don't recall a civil war quest sending me to morthal or Dawnstar but I guess experiences can vary depending on if your also doing season unending for the MQ and have different holds to take back.

Ahh! Another one I had not gone through

Morthal (SC) and Dawnstar (IL), if Season Unending was never initiated. Of course with SU, depends on the negotiation.

I know of two:

Ah, yes. Forgot about that Inn Keeper rumor