For the roof shakes we'll create another pixel pattern with colors from the BROWN swatch.
Create new image, 48x24, filled with medium brown (brown swatch, 3rd from left).
First we'll set up some guidelines to help draw the shingles.
View > Change Grid, Guide & Snap Properties > Current image settings
Horizontal 12, Vertical 8 pixels, any contrasting color.
Click OK, then select View > Grid (on).
1. Using the Grid guide, paint some lines to represent the roof shingles. Use the darkest brown from the swatch. Don't follow guidelines precisely; randomly stagger alignment and make each shingle a slightly different size. Paint these roof shakes with a 'shaky' hand. In other words, be loose and irregular with the lines for your best imitation of wood shakes. See example here.
2. Zoom in close and paint the LEFT and BOTTOM edge of each shingle. Use lightest brown from color swatch and paint it next to dark brown line with an extra pixel in some of the corners.
3. Paint a shadow line on each shingle under the dark brown line. Use color #4 on brown swatch. Paint 2 rows of pixels.
4. Let's make the shake pattern more subtle by randomly removing some of the lines. Grab the Paintbrush and randomly paint over some of the lines using the original brown base color. Add some more shadows and highlights wherever you feel some are needed.
5. Our pattern is starting to look like shingles! Let's create a bit more irregularity by adding noise. Same settings as before. Adjust > Add/Remove Noise > Add Noise
Return to cottage HOUSE layer. Load ROOF selection from alpha channel.
Flood fill the roof with the new pixel drawn shake pattern.
The last step in finishing the roof is to change the color of the black outline to match the rest of the roof. Zoom in to 800% and load the OUTLINE selection from alpha channel to mask the outline as you paint.
Tip: Hide the 'marching ants' marquee when working with such small selections. It will be easier to see what you're doing! Selections > Hide Marquee
Use light brown along the top ridge, a medium-dark brown on the side, and the darkest brown along the eaves. If you erase 2-3 pixels of outline between shakes it will add to the realism. You could also put a few darker pixels between some shakes.