Backup files at the end of the day
Doing multiple imports on the same line from different modules is frowned upon by PEP8, Python's official style-guide.

It also recommends using lower_case for variable names and not camelCase.

You don't need () around variables when assigning, src = 'C:\AEC Work\' + newFolder is enough.

Since you are already using os.path.join, which is a good thing, you should use it throughout.

You can use str.format to get "{:%m%d%Y}".format(datetime.datetime.now()) for the new folder name to make this slightly more compact.

import shutil
import os
import datetime
import time
import sys

os.system('TASKKILL /F /IM FlashRen.exe') 

now = datetime.datetime.now()
directory = "{:%m%d%Y}".format(now)

src = os.path.join('C:','AEC Work', directory)
backup_base = os.path.join('\qnap01', 'Data Service', 'AARON')
dst = os.path.join(backup_base, "{:%Y}".format(now),
                   "{:%m. %B}".format(now).upper(), directory)

for file in os.listdir(src):
    src_file = os.path.join(src, file)
    dst_file = os.path.join(dst, file)
    shutil.move(src, dst)