Why do my apps open in a single space when resuming?
Not certain in Yosemite, but in Mavericks apps would only restore to the Space they were on if they were set to specifically open in a given Space - otherwise they would all huddle together on the front-most Space at launch.

Right click the app in the dock to set to 'This Desktop' once you have it in the correct one.

Quickly move an app to another Space by left-click-hold the top bar of any window then hitting your key-combo for the desired Space.