I assume that you've already added your domain to Google Apps. At this point I'll assume you'll want to set up e-mail for the domain administrator (which you selected on registration). You can add more users in Google Apps and you'll need to go through the gmail specific steps for each one.
To have email work for your Google Apps domain you'll need to set up the MX records with your domain name registrar's control panel. If you are with Godaddy and you were using the domain with a different host, be sure to "park" the domain and wait a few minutes the go back in to the domain manager for your domain to edit the zone file.
Here is the table from one of the Google help pages. However another says to set the priority to 10,20,30,40,50 instead of 1,5,5,10,10 so it really doesn't matter.
in the MX records add the first one and if your domain registrar lets you add the others. Set the time to update to around an hour, but again that really isn't crucial.
Save the settings and go to the Google Apps email page to verify everything. The Google Apps set up also mentions the settings for mx records so no problem. The important thing is to get the servers added.
After everything is saved you'll have to wait a while for the DNS records to populate for the gmail account to actually work.
Now go into gmail. gmail.google.com or mail.google.com both seem to work. Log in with your Google Apps user name and password. If you are logged in with your regular account you'll need to log out first.
On your first gmail log in you'll have to accept the user agreement. Next go to settings. It is either at the top of the new e-mail message display or at the top right corner of the page.
After clicking on Settings go to "Forwarding and POP/IMAP". Enable either POP or IMAP and click on "save changes".
At this point, you'll need to configure your e-mail client software.
Your user name is your complete email address.
The password is the password for the user.
For outgoing e-mail use:
For incoming e-mail use:
Use SSL: Yes
Port for TLS/STARTTLS: 587
Port for SSL: 465