Sorry Chad on how I explained it. I know what you are after. I been doing it for some time and love the ability to get all my mail in one location.
Domain Alias
If you use 1 google apps account and put all your customers domains on it, then each google apps user will get an email address with each domain name assigned to the google apps.
Example
Domain1 owner was named Sarah Giggles and her username is sarah.
Domain2 owner was name George Smiles and his username is george.
Each will receive the following email address automatically:
Sarah Giggles gets sarah@domain1.com and sarah@domain2.com
George Smiles gets george@domain1.com and george@domain2.com
Let's say you opt not to tell them about the other email address, but then all of a sudden they got email address to their username@theothersdomain.com. Not very professional and it puts a question mark in their brain on how reliable you are in setting things up.
What I recommend, Just my opinion:
First set up a google apps account for Your Business Domain(not your customers) then choose A or B:
A. For customers who do not plan on using email address with their domain in it:
Log on to your customer hosting server and create a forwarding account for the email you want to use. Then forward it to your google app for your website domain.
Then in your google apps for just your domain, you can create a setting that allows you to send mail as the email account you set up on your customer server. Then you get mail from their website and you can switch identity to their domain to send mail from your google apps.
It is clean and simple and if some day they decide they want to have their own google apps, your not trying to undo a bunch of stuff.
B. For customers who might or want to use their domain name in their email address:
Set up google apps for just their domain. Then create all the email accounts; yours, your customer and so on.
Then log into your email account on your customers google app and forward it to your google app for your domain.
Then log on to your google app for your domain create a setting to allow you to be able to send email as the other email account with your customers domain name.
If your customer already has an existing gmail account, you can still set up the customers google app user account to forward to their gmail and also they can create a setting to allow them to send mail using the email address from their domain too.
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Chad, Domain Alias work great if you have a business with many identities, but I don't recommend locking your customers domain names up. It is easier to take a bit of time in the beginning and then there is less mess to clean up in the end if things change.
Have you used Gmail and their settings for allowing you to send mail as other identities?