Generally, you would want to do one of:
a) Keep any code that you've pulled in from another project in its own directory structure with a license file indicating where it came from and its licensing terms.
b) If you intend to modify the code or integrate it more tightly with your own, copy the notice into each source file that was taken and perhaps put a pre-amble along the lines of "Portions of this file were copied from XXX under the MIT license as follows:". Ideally you would make a commit with the file in its initial state as copied, and then if you ever need to determine what came from where and how it was licensed, it shouldn't be too difficult.