HI BikerBob38,
On my set up iMessages is the top Account.
This is because when I installed th Beta in Lion you had to Set up the Apple ID first before the app would open.
It would then "load" those AIM, Jabber and other ID that were present in System Preferences > Mail, Contacts and Calendars and set to work with Messages.
The Order only effects two places.
The Messages Menu > Accounts where the Logged in one are ticked and you can log in or log out the accounts (selecting each toggles the setting to remove or add the tick)
The other place is the Window Menu.
In it's default setting this will list all Non iMessages accounts under "Buddies" with the CMD + 1 Keystrokes.
If you go to the General Section of the Preferences you can unlink them.
The Window menu will then list them in the order they are in the Accounts Preferences minus wherever the iMessages Accounts is.
Combined pic of General Section setting, the Window Menu in drop down and two Buddy lists.
The Buddy List "Name" or title will be either the unchanged Screen Name of Jabber ID if you have only one (of each) or it will be the Screen Name or ID itself unless you add a Description in the Preferences > Accounts
From there you would normally have a Buddy List open.
You can use the Buddy list the same way you did in iChat, double click to start Text Chat or click an icon to start Video or Audio or Highlight and select the Screen Sharing Icon.
The Text Chat are added to the Main Message window (Tabbed Chats and main Interface - Window Menu "Messages" CMD = 0)
Once there the "To" spot at the top of the Messages window becomes a drop down if you have any other Info on the person's Contact Card (Formerly the Address Book).
If they have an iMessage Name you can swap to AIM or from AIM to iMessages.

Link if it will not display
In Messages > Preferences > Accounts you are right that the list can be reordered.
However this is only done for your own viewing pleasure. It makes no difference to the operation and function of Messages.
As with regard to Points.
I always say "Thank you" (Mainly to highlight what the Tick and Star are for)
Only the Original Poster can award Points, to a max of three posts in a Thread (two "Helpfuls" and a "Correct")
If I were that serious about Points I would be worried about my Post to Point ratio (Not they tell you how many posts someone has made in the current software).

8:24 PM Friday; October 12, 2012
Please, if posting Logs, do not post any Log info after the line "Binary Images for iChat"
iMac 2.5Ghz 5i 2011 (Mountain Lion 10.8.2)
G4/1GhzDual MDD (Leopard 10.5.8)
MacBookPro 2Gb (Snow Leopard 10.6.8)
Mac OS X (10.6.8),
Couple of iPhones and an iPad
"Limit the Logs to the Bits above Binary Images." No, Seriously
Message was edited by: Ralph Johns (UK) Having issue with Evernote stored Pics