[quote=@scribz]
<Snipped quote by Sherlock Holmes>

Haha oh god. Dude I have fl.ux on my laptop. So when I was colouring it was under a red shift tone. What I'll do is get Photoshop to edit the tones. 

I'm still not comfortable just straight up adding colour strokes on, so do it all in greyscale and then use a screen layer on top. 
[/quote]

That's part of your issue -- don't use 'screen' to color. Use 'color' to color. Or 'overlay'. Or 'multiply'. Screen ups all your values and washes things out. The other options will keep your contrast and, depending on which one you choose, even add to it.