Please make sure that your Apple Mail account is reading from the CRX Local POP Server.
Before your e-mail from your POP server(s) (inbound e-mail) went :
POP Server ==>> E-mail Client Software (Apple Mail, Entourage, etc...)
Now it goes:
POP Server ==>> Em@ilCRX ==>> Email Client Software (Apple Mail, Entourage, etc...)
Your SMTP Servers (outbound e-mail) function as before, with no changes required to your E-Mail Client Software settings for SMTP server.
If the settings that you are using in Em@ilCRX are correct, e-mail should be going into the Em@ilCRX database.
From the Em@ilCRX database, it is distributed to your E-mail Client Software via the Em@ilCRX Local POP Server.
There is now a user manual at
http://www.emailcrx.com/instructions.htm, that has some graphics, and further instructions that might help.
Basically, the only thing that you should have to change is the POP Server in your Email client software so it matches the configuration in Em@ilCRX.
Then configure your Em@ilCRX Local POP Server so it matches the settings in your Email client software.
Then add an Account to Em@ilCRX, that is configured EXACTLY like your Email client software was configured, so Em@ilCRX can read your POP server, and send abuse complaints and challenges.