In the EB apps where I have users performing edits, I have pop-ups enabled as well. To perform edits, users have to click on the edit widget, hit the select button, and then click on the target feature. In my case, this causes the edit pane to open instead of the pop-up window.
If you want to control which layers have pop-ups enabled, I believe you would disable pop-ups in the web map for the editable layers, not in the EB app. Some EB templates also allow the user to disable pop-ups for individual layers in the Map Layers widget, but it sounds like you would rather spare your users the effort.
