I have two mail accounts set up (one xyz@me.com, which I'll call account 1, and a second that is a google apps account, I'll call that account 2).
Mail App-->Composing-->Send new messages from:
Account of Selected Mailbox
In this setting, if I unhide the Mailboxes pane at the left of the mail window in Mountain Lion and select the account 1 mailbox, then click the 'Compose New Message' icon, a message is created using the mailbox selected in the Mailboxes pane.
If I change the selection to account 2 in the Mailboxes pane, then click the 'Compose New Message' icon, a message is created using that account instead.
If I reply to any message the reply goes from whichever account the person sent the message to.
If I create a new message and no mailbox is selected, it appears as though the first account in the list of mailboxes is used.
Specifying an account in 'Send new messages from:'
If I specify either account 1 or 2 as the default for 'Send new messages from:' the a new message is sent from that account regardless of which mailbox I have selected. Likewise, if a create an email from outside the email app, the specified account is used.
This seems like correct behaviour to me; I'm quite happy with it anyway.