There are a couple of ways of doing this. The easiest is probably to just add the secondary address in the Mail.app -> Preferences -> Accounts field.
The specifics of which vary a little based on the OS/Mail.app version you're running, but in Yosemite:
Mail -> Preferences -> Accounts
Select your iCloud account and change the 'Alias' popup menu from your iCloud address to 'custom'.
Doing this enables the 'Email Address' field. In this field you can enter the email address you want to appear in your From header.
If you want to use multiple addresses (e.g. your iCloud address and your other alias), you can enter a comma-separated list of addresses - e.g. 'you@mac.com, anotheraddress@otherdomain.com' and then you'll have a pop-up menu on each new message where you can choose the address to use for each outgoing message. You can also set the default address in Preferences -> Composing -> Send new messages from: