The way I used to work In ESRI was to create an .mxd with various layers and publish to ArcGIS Server. I would then create a web map selecting whatever layers I wanted to show.
Now, with ArcGIS online if I go to my content>add item>from the web>'ArcGIS Server or Web Service' by pasting the service's URL it adds all the layers from the .mxd but as a map image layer rather than a feature layer. I now know that if I want to use my data with web apps I have to load my data as feature layers but this means adding an extra /0 at the end of the service URL thereby specifying the individual layer. Do you have to load every layer one at a time for it to be recognised as a feature layer?