I have more than one e-mail account on my outlook. How can I specify which e-mail account to use to send my merged e-mails?

There is an option to Send using this Account: at the last step of the wizard. You can choose the desired account from the drop-down menu.

In EmailMerge Pro Version,  there is an option to send on behalf of (Microsoft exchange users only) on the last step of the wizard. You should have sufficient permissions to send on behalf. If you choose an account for which you do not have sufficient permissions than the default user is used automatically.