There are a few ways to do this.
First, you can take a look at handling uploaded files from the Django docs. If you read it over, basically you can handle the upload of the file within your view in the same part where you are processing your form.
Another option, and one which I think would be better is to use a custom file storage system. You could do this very simply using the existing one as a base but simply change the location, then use it as an argument in your FileField. For example:
from django.core.files.storage import FileSystemStorage
my_store = FileSystemStorage(location='/some/other/dir')
class SomeModel(models.Model):
file = models.FileField(storage=my_store)
Hope that helps!