Yes, it's possible, in fact, it's encouraged. You will need to create a different file for each pool you are running.
First thing is to get the correct teams file, in your case you will need to download the NIT bracket.
The only real hangup might be, if you are using the database option to import brackets (and you should be), you need to set a UNIQUE index for each file. (See the Database Settings when creating a web form or when importing brackets)