For my design, Ladyada challenged me to make the yellow portions copper colored rather than printed yellow. 

The JLCPCB process only offers ENIG coated, which means exposed copper will have a very thin gold plating. Gold seemed good!

I edited my bitmap to make the yellow squares transparent and specified that silkscreen should not be in those areas.

I thought I put in the copper layer but after two rounds with JLCPCB engineers, apparently the Gerber file did not have the front and back copper layers. Drat.

As the unexposed areas will be silkscreened, specifying the whole copper layer as copper should be fine. For a two sided design, be sure to put copper on the front copper and back copper layers.

Select the Copper Pour tool shown above. Draw a box around your design. You then specify the copper pour name and which layer you want it on.

Removing the Solder Mask to Expose the Copper

Setting parts of your PNG to transparent prevents printing, but you'll need the solder mask removed to see the copper. 

Click on the Top or Bottom Solder Mask layer at the right and then draw a filled region with the tool to the right of the Copper pour tool.

Seeing the Bare FR4 board

As I made a mistake and did not put in the copper pour but did remove the solder mask, my two areas did not have copper but showed the yellowish FR4 base board. Yikes.

But it worked out as I was looking for a yellow color and the board is yellow(ish). Note that the ordering process says a black board - that is not what I received.

Also in 3D and 2D views, the removal of the solder mask looks like the copper layer is visible. This is deceiving as this is the FR4 substrate.