Hello, that is a good explanation of what we need to know, it does help to understand the question in detail, so we can figure out where you are stuck
What you have is four sealed threaded holes on the roof, the dimples, two per side. They are sealed with a mastic and painted over in the factory that dries and has hardened up, so it is weatherproof. These were hidden by the plastic strips which you have now removed.
You need to cut round the mastic at each of the four dimples with a stanley knife (see video, cut round the dimple in a rectangle shape), then peal the mastic off, use a flat edged screwdriver to dig it out. If you think you have exposed any paint (try not to) and see bare metal, then paint it to prevent rusting.
Now you have the four threaded holes for fitting the supplied bolts from the roof rail kit which will be the correct size of thread and then fit the roof rails. I would put some silicon sealant on the top part of the threads under the bolts head when inserting, to make it completely waterproof. Do not overtighten or you may strip the threads. Hope that's you sorted now. Cheers.
Here is a Generic Ford video (not Ecosport) that shows a guy cutting the mastic away, to give you a better idea how to do it....