Yeah MT Manager works in a different way, you will navigate to an apk and open it, then once you are done you can repack that same apk or recompile a new one.
Im sure there will be some good guides on here somewhere, but you will find your own way of working with it.
I like to find the images/files i want to edit, extract them to another folder, then go make the edits in windows, then go back into MT and replace the original files with my new ones.
If you want to change the app name, you will need to search within the dex files and resources via the included tools and make the changes within the app.