Sorry, the manual is for the old email-based system. There isn't a manual for this verison yet, aside from the other thread in this very forum.
Okay, to move your vehicles, make sure you are logged on, then mouse over your ships. You'll see an 'orders' button if the ships hasn't received orders yet this turn.
Oh, and you *must* be using Firefox 3.6 for best experience, although Chrome 7+ seems to do 98% of the display correctly now, thanks to work by Wedge, and even IE is now 'playable' although still ugly. I can't compare against Opera or any other browser since I don't have them, but Wedge has done work to make it at least playable with them too.