(this is for digital comics stuff) Ok... I've painted my pic by setting the lineart to multiply to make the white areas transparent, painted all the colours underneath this layer and then gone to flatten it WITHOUT INCLUDING THE BACKGROUND LAYER/S When I do so the original lineart goes back to 'normal' mode and all the white areas lose their transparency and revert to white and I can't see the colours anymore that were underneath. How can I do this and yet retain the transparency in the lineart layer? If I flatten the image with all layers included then I don't have the problem. But sometimes I want to take just the lineart and coloured pic and put it on a different sized background. (eg - for a desktop image) I know that I could use an alpha channel to set the lineart layer in the first place rather than setting the original mode to multiply but there has got to be a way to what I want. How to do it though????

Don't flatten the layers. You need to Layers > Merge visible to retain the tranparency.

Dreamer's method is the quickest way to retain all layer effects. This is also what I use. Without considering the size of the file, I always stamp visible onto a new layer. This retains all previous layers that I may need to go back and tweak.

Scratch what I just said. I stamp visible onto a new layer, not merge visible. They both accomplish the same thing, retaining layer effects, but stamp visible keeps all other layers. Merge visible, merges them into 1 layer.

dreamers method works for me

Link the layers & Ctrl+E (Merge) not merge visible