Alejandra,
You mention a WMS service. Are you referring to the fact that when publishing your service you checked the "WMS" box in the Capabilities list or are you using 'WMS' as a generic term for the service?
If you are publishing and sharing the service as WMS I will be of no further help, as I have never needed to publish my services in that way. Hopefully someone else on the forums can respond or perhaps this warrants a support call to ESRI.
If you are using WMS generically, in the Capabilities list for services that have editing capabilities I check the "Feature Access" capability. This enables the geometry to be served up via the FeatureServer service that shows up in your services list.
As for the data layers being edited... I use data layers from my SDE data store, versioned for editing with the option to move edits directly to base (the checkbox in the dialog that pops up when you register a layer as versioned). I am using direct connections to the SDE database. I create a child version that will be used for the editing in my flex viewer in ArcMap. Then in ArcToolbox I use the "Create Database Connection" tool to create a connection to my SDE database **that connects to the version that I am using for editing**. That tool allows you to specify a particular version. I save that connection in a place where my Server can access it.
I then start a new ArcMap project and connect to my SDE database and add my layer(s) that I am editing within that version. You may need to start editing and ensure that the layer templates are set up. I typically add a feature of every type that will be edited just to test but also to verify that the editing app is "seeing" everything. I delete these features later before actual use. I then publish the map as a service with Feature Access checked (as described above).
After the service is published, I configure the edit widget as well as the main flex viewer config file so that my layers show up. I typically create a separate version of my viewer specifically for editing a particular layer or set of layers. I like to have my users in the habit of consciously editing or consuming data but not blurring the two use cases together. After all, if they are the stewards of the data, I want them to be successful and not inadvertently introducing errors into the data. End users that edit data don't always think about the big picture of their actions like those of us that "do GIS" do. That means their regular, departmental viewer has the layers that they edit but doesn't have the editing function added. If they need to add or change anything with that layer they must load the editor, which I tend to strip down to the necessities for editing and not everyday use. But your specific needs will dictate how you structure everything.
If your map services are public, share the link and we can take a look. Maybe something will pop out that hasn't been obvious in our dialog.
