You will want to make sure the Subject of the email is correct.
Example would be: Incident# 12345 (where 12345 is the actual Incident Number). You can have other text in the Subject as well, but must have 'Incident# 12345' in the subject line.
If it is not formatted that way, then a new record will be created when an email is received unless you have modified the application to look for something else in the Subject line.
Thanks Paul for your help. I'm good to go now.