When you hit reply to something, it should give you an option to "Meme Comment."
If you click that, then you can make a meme in the comments with one of the popular templates, no problem (or you can also choose from any templates you've previously uploaded to imgflip by opening the My Templates tab, and it should still come out).
If you want to make a meme comment with a picture that isn't a popular template or a template you've uploaded before, just click Upload Image after you've clicked Meme Comment, and make a meme as normal.
If you want to have a comment that has text and a meme at the same time (like this one is), you type the text first before clicking Meme Comment.
That should just about cover it (I think!) Try it out if you want to, then let me know if you have any other questions. :)