AppleScript to move selected Mail messages to a particular mailbox of a particular account. User is asked only once. [This script](https://gist.github.com/Zettt/6551617) let's you choose an account first.

Move Mail Message Multiple Accounts.applescript

(*
Mail Filer
Files messages in Mail.app using type ahead. Displays one dialog containing all mailboxes and accounts.

Created by Andreas Zeitler on 2013-09-13
Copyright Mac OS X Screencasts 2013. All rights reserved.
*)

set myMailboxes to {}

tell application "Mail"
  
	-- assemble a list of all mailboxes of all accounts
	set allAccounts to (name of every account) as list
	repeat with thisAccount in allAccounts
		set theseMailboxes to (name of every mailbox of account thisAccount) as list
		repeat with thisMailbox in theseMailboxes
			set the end of myMailboxes to (thisMailbox as string) & "\t\t\t" & (thisAccount as string)
		end repeat
	end repeat
	
	-- present list
	choose from list myMailboxes with title "Choose Mailbox…" with prompt "Please select one account" without multiple selections allowed
	set chosenMailbox to result as string
	
	-- split mailbox and account from result
	set oldDelimits to AppleScript's text item delimiters
	set AppleScript's text item delimiters to "\t\t\t"
	set mailboxAndAccount to every text item of chosenMailbox
	set AppleScript's text item delimiters to oldDelimits
	
	-- these are the mailbox and account we need to move messages to
	set chosenMailbox to first item of mailboxAndAccount
	set chosenAccount to second item of mailboxAndAccount
	
	-- move selected messages to chosen mailbox of chosen account
	set s to selection
	if s is not "" then
		repeat with currentMessage in s
			move currentMessage to (first mailbox whose name is chosenMailbox) of account chosenAccount
		end repeat
	end if
	
end tell