To send a sequence from an alias or secondary email in the CRM, click the drop-down next to the From field and select the email address. You can then click the Sequences link to select and configure your sequence.
A secondary account is another unassociated email address you may have. For example, you can connect your personal Gmail account to HubSpot (a different account than the one paying for HubSpot Sales Pro) and send a sequence.
The email address set up in your user settings doesn't necessarily need to be the email address you are using to send sequences. Your user email address may be an alias as long as you have an inbox connected to HubSpot with the alias configured.