I assume she wants to manually upload because the due date has passed for the assignment, so the student cannot upload himself.
You can do this as follows:
Go to the assignment page and note what the assignment number is (it's a number that varies for each assignment and is typically 4 digits long; if you're not sure which number it is, check a few other assignments and note which number in the file path is the same for all of them).
Then mouse over the student and get his number as well.
Now, from the class page of the moodle, go to "files" and then select "moddata" and then select the proper folder for the assignment according to the number you found above.
Peruse the folders and see if the student has a folder named after his student number. If not, create it.
Next, deposit his assignment into the folder with the "upload" option.
Finally, go through the normal interface to the assignment page and ensure the student has the file(s) you uploaded correctly listed under his name.