After you import the Episodes with their embedded Cover Art into MC, select one Episode (any) and right click it. Then select "Cover Art > Get From Internet..."
You will be presented with a dialogue that allows you to select the image you want to use for the whole Series, and for each Season. MC will look up the image online, and will also show you any image that already exists in the Cover Art directory structure. Series and Season Cover Art images are always stored in the Cover Art directory structure, but that is what you want anyway, so all is good.
If you want to use your own Series and Season Cover Art, put the files into the correct Cover Art directory structure and name them correctly, and MC should find them.
Your Episode images should remain untouched, and displayed correctly. You must have the correct settings for that now, since the images are being found and used. That is, assuming that it is the embedded image that is being displayed, and not a screenshot from the MP4 video file. ( "Options > File Location > Cover Art > Also store image in file's tag" ) I can't test your scenario as I use a separate image file, stored in the same folder as the video file, for my Episode images. The "Get Movie & TV Info..." function retrieves those image files and stores them in the correct location. I assume you are providing your own Episode images, and don't want the "Get Movie & TV Info..." function to retrieve images, so make sure that box is unticked if you run the function, or the image tag will be overwritten, and possibly the image in the MP4 file itself.
If your Episode images do get mucked up, and that can happen, explore using the "Cover Art > Quick Find In File / Cover Art Directory" function. I often get a screenshot as Episode Cover Art, I think because the import doesn't override an existing image tag. I fix that with the "Get Movie & TV Info..." function.
Note that Season level images are only show in Theatre View once you have at least one Episode in at least two Seasons. Otherwise MC jumps from the Series level directly to the Episode level.
The import process will usually/sometimes retrieves the correct Series and Season images, but I find that it often doesn't. I don't know why. Sometimes it just takes a little time for MC to retrieve the art, maybe during a later Import run. So I just run the "Cover Art > Get From Internet..." function to add missing Series and Season Cover Art. When MC doesn't have Series and Season Cover Art, it will use any art it finds in the first file for a Series, and if there is no image for that file, it will use a screenshot from the video.
See how you go with all that.