If you are using any of the Communications options available to you--Message Templates, Opportunity-specific Communications, or creating Ad Hoc Emails--the system will automatically send these communications to whichever email is designated as the Primary Email. There is no option to submit these communications to additional Email Aliases as listed for the User, or to input these other email addresses directly into the email recipient field.
In order to send your Communications to any email other than the Primary Email, you would have to create and send your communication outside of the system.
You may also want to utilize the Banner notifications for things like award offers, post-acceptance requests, and other communications that require action, and for which you want to ensure the applicant sees them and acts on them. These will appear in the applicant portal, and therefore not be determined by email address.