I was traveling on foot just looking around and I found what looked like a alter between two bridges. On the alter there was a dwarves sword, helmet and in front of the alter was an empty chest. I put them put in the chest think something would happen but nothing did. Does anyone know what the deal is with this chest? I thought it was weird that it was empty...

On a side note further south from here was some ruins (forgot the name) but it had some enemies that were infected, that spit green smoke or something (they were human) the entrance was blocked with roots or vines. How do I get inside?

If it was called a dwarven convector then it's involved in a quest. http://www.uesp.net/wiki/Skyrim:Arniel%27s_Endeavor

I've seen ruins like these with the same type of folks, Afflicted I think and also the covered door. At the base of the stairs there was a switch to turn on the propeller blades. No idea how to get in.

Yea, that is the place! There was another door here but it is locked and none of the guys I killed had keys....I guess that is a quest too.

That place is for the Peryite deadric quest.

Yep, Tha'ts it! Thanks!