alias youremail@me.com(icloud) from a custom domain (like Google Apps fyd)
iCloud is just IMAP under the hood.  It's not possible using the default configuration to use an email address that is now supplied by iCloud (whether using the old me.com or the new icloud.com), but it is possible to configure in a non-standard way to achieve the same effect, but it does require the use of a 3rd party SMTP server to achieve this.


Basically, on your device, setup iCloud as normal.  Then amend the preferences and turn off Mail and Notes
Then, in Settings > Mail, Contacts, Calendars choose Add account > Other > `Add Mail Account
Enter your Name, the email address you wish to use, the password of your iCloud account and a descriptions along the lines of Custom iCloud Mail then Next
Leaving the top details as you entered them, and ensuring you stay on the SMTP tab, not POP, enter the following in the Incoming Mail Server fields:


Host Name: imap.mail.me.com
User Name: Your iCloud username as the full email address
Password: Your iCloud password

In the Outgoing fields, enter the details of your SMTP server, you may use gmail server addresses in here if you have a GMail account, or use a paid hosting company like I do.
Click Next, and it will attempt to verify the details.  Hopefully it will all work fine, and put a load of ticks next to all your inputs


That's pretty much it, you now have iCloud configured normally for everything except mail and notes, and mail should send through your own servers allowing you to use what you like as your email address for return purposes.  Don't forget to forward all your mail to your iCloud account.  Sent mail will still remain in your iCloud sent mail folder, regardless of the fact that is is being sent through a 3rd party server so there is no need to bcc yourself to keep a copy, unlike with some other solutions.

One last thing, why include notes and exclude them from iCloud?  Because notes are just mail items stores in a special IMAP folder.  Turn them off in the new manual account you created, and you will see the Notes folder appear in Mail.app.  Turn it on, and that folder is hidden and the notes are shown through the Notes.app instead!  However, you will end up with duplicates, unless you turn off your iCloud version of the same folder.

Things to note, you can use this setup for pretty much any normally unsupported mail client, including the one in iOS4 etc in say in iPhone 3G