Has anyone developed any particular "tricks" when using aftermarket wooden decks like Prontos'. Has anyone for example tried staining individual planks to break up the appearance?

I've never done this but this is what came to mind when I read your question.

To vary wooden deck planks one way would be to stain the desk with the lightest color first. Then apply masks to individual deck planks to cover the light colored stain. Then apply a slightly darker stain. Mask more exposed boards and repeat this process. Time consuming but would give you that varied pattern. Then maybe a overall wash to blend together if needed and highlight the space around each board.

My thoughts too. I guess it depends how much bleeding will occur. I was thinking maybe using colored pencil.

But the wooden deck has a natural divergence in colours. Why would you buy a wooden deck just to have to paint individual planks again?

because it is made from a single piece of wood, it as a degree of sameness. I think just a few planks, subtly different would make a difference in the more open areas of the deck.

There is a water based stain that comes in black grey and brown. It is called "The Detailer" ....ready to use washes. Brush it on give it a bit then gently wipe off the excess....highlights the scribing very well. Won't do indiviual boards but you can brown wash one area and black another. I guess you could paint individual boards but I ask if you are going to do that why buy the wooden one just do it on the plastic.

Oh this stuff works well on all kits....highly recommended I think it was Dade that told us about it.

I would really like to leave the decking 90% alone. But I thought it might improve in a tiny bit here and there, to have a plank slightly different in shade. I'll have to experiment on some scrap. My main concern is bleeding into unwanted areas. I suppose I could mask a few random planks, seal the deck with flat clear and the stain the masked areas and reseal. My goal is to be subtle.

Kurt, you will find that many wooden decks actually have divergence built in. Well they have enough for me in 1/350. Most of the ship I have seen have mainly the same colour planking anyway, well in 1/350 anyway. Good luck in your search.