I have a script that reaches out and touches my mail server and then alerts me that I have new mail. How do I make sure that my Inbox (titled ‘In’) is highlighted before all this is done and not, let’s say, my ‘Sent’ box?

Simple enough:

tell application "Mail"
	tell message viewer 1
		set selected mailboxes to {in mailbox of application "Mail"}
	end tell
end tell