Photomerge in Photoshop CS4E?

The Photomerge in Photoshop CS4E is a fantastic tool when it gets it right, but what can you do when it doesn't? I've got a bunch of 9 images (in a "Noughts and Crosses" or "Tic Tac Toe" layout), all with 50% overlap, but a lot of fairly blank areas - this can't be avoided, they are nautical charts.
When I do Auto Photomerge on these, a couple of the images get put in the wrong place. Is there a way to position the images in their approximate place, then get Photoshop to finish the job automatically?

Hi Zeno,
Many thanks for that, it certainly helped. The plug-in let me position the layers in the right place, but of course I lost the ability to use "Auto".  I had spent all afternoon doing it manually on one output file: locking layers, blending, saving and re-loading!
I think the manual mode will be good enough for the current project, but it's a pity you can't say - "this is roughtly where the layers go, now look again closely for the overlaps and finish it automatically" 

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