All my tanks use masking (or rather, templates) for the paintjob.
You can see the base layer has areas cut out from it, and is then duplicated for other layer manipulations. Making a new skin is as easy as recolouring/redrawing patterns on the base layer. I didn't explain in detail other than that they should mask out parts they don't want painted, I leave the actual masking method they want to use to whatever's comfortable with them I only mentioned that they ought to lock the layer's transparency once they're done masking to make the job easier.
I used to do your way of separating the different colours, but I like to keep my layer manipulations simpler. Besides, I also like hand drawing my patterns. If I want a new skin I just reuse the template but draw a different pattern scheme.
Instead of manually "knocking out" each colour layer you can put all the colour layers into one layer folder, select the layer folder then click on the create layer mask button (look at the image below, it's the button next to the fx button at the bottom of the layers panel - the one with the circle inside a rectangle). Go back to your blue layer and make the selection on the uncoloured parts, go back to the folder's layer mask and fill the selection with 100% black.
This way you only need to do it once, plus you can edit the layer mask without altering the colour layers within the group. However with my skins I start with only one base layer and have all my colours in it so I don't use the layer mask for this purpose and only duplicated the base colour layer if I want to add other layer blending modes.
I suggest using "Blend If" to get those darkest parts to show (plus it'll let you fine tune how much of it you want). The advice of using auto-contrasted base layer is good however I'd recommend using curves or levels instead to adjust the contrast to your liking. I avoid anything with the word "auto" in it =P