As for the "Eye controls Shadow forces..."
I always had the impression it was not so much controlling the ships, but sending them their orders - as part of it's function as the Shadows "great machine", it controls Z'ha'dum's defensive systems, various internal stuff and the main communications...
And as for "Eye active after Galen"
<table bgcolor=black><tr><td bgcolor=black><font size=1 color=white>Spoiler:</font></td></tr><tr><td><font size=2 color=black>Remember - a long time ago the Shadows themselves had to serve as controllers for their ships and other big installations - in ancient times when there were no younger races to use instead. They probably did it in a way similar to Galen's temporary joining with that ShadowShip, as partners instaed of slaves.
So there would be nothing to stop one of them to step in and personally assume control of the Eye (at least until they can prepare another suitable slave - though in this instance they probably went beyond the rim before that happened...)</font></td></tr></table>
And finally as for "Shadows & Order"
<table bgcolor=black><tr><td bgcolor=black><font size=1 color=white>Spoiler:</font></td></tr><tr><td><font size=2 color=black>Invoking Darkness p.327: It is only at the meeting of knowledge and ignorance, of light and dark that new understanding may be found: in the shadow. Say "meeting of order and chaos" instead and you have the true philosophy of the Shadows - the way they lost in their struggle against the Vorlons. Not only order, because it prevents innovation; not only chaos, because it destroys as much as it creates. The truth lies in between...</font></td></tr></table>
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"ShadowScout"
Roman Alexander
"Go on, watch out for Shadows - we'll watch you right back!"
What do you want?
ShadowShips!