First, when writing a paper, always follow your professor's instructions and requirements.
Second, the MLA Handbook can't cover everything. Don't get frustrated if the Handbook doesn't cover the exact thing you're looking for. Be flexible. In the absence of something being covered in the Handbook, the best advice is be consistent. If you choose to do something your own way because you can't find guidance in the Handbook then be consistent in that paper and always do things the same way.
Finally, there can be a lot of value in communicating with your professor: ask them questions about sources and style; keep them informed of issues and difficulties you are encountering; and point out situations to them before handing in the paper. Doing this also lets your professor know you as a researcher and author are aware of an issue. This type of communication is much, much better than not saying anything at all.