If the vampires are doing something so drastic as to block out the sun why don't the dawnguard get some back up from the imperial army/stormcloaks?

I would probably put my thumb on two reasons...
-The Empire is already too busy with their own civil war with the Stormcloaks, likewise the Stormcloaks with the Empire and have bigger things to worry about than a bunch of Vampire Hunters rambling on about Vampires trying to Eclipse the world.
-The Devs didn't program it as such.

- They might actually get backup from the winners of the Civil War, but the Dawnguard's leading the charge.

Perhaps they're too proud to seek help from outsiders. They probably feel as though they can handle it. My opinion of it anyways.

I can see that happen. (I also hope the DLC for Skyrim is going to have links to the mian quest and other DLC. Kinda like how the DLC for New Vgas has links to the main quest.)

I don't find your question to be stupid at all, I'm sure the dawnguard will be fine.

Look at it this way, the side you join, is the side that wins.

What if you don't choose a side but find a nice place to sit and read the "Lusty Argonian Maid" like the fellow in your avatar?

Then you still win.

Well in that case, events do not transpire.
Remember the ancient words of wisdom as spoken by Zurin Arctus, the Underking himself in the opening to Morrowind...
""Each event is preceded by Prophecy. But without the hero, there is no Event."

Without us the Player to see history happen, it simply doesn't happen, the actors awaiting in the wings to take their assigned roles, awaiting the star to take center stage.

Because not everyone knows [censored] about to go down.