How do I ground a light fixture with two ground wires and only one ground at junction box?
In a single circuit, all ground wires and metal fixture structural parts are connected.

In your case, the green wire is the ground for the lower part of the fixture. The bare wire is the ground for the metal canopy. The green screw is the ground for the fixture bracket. The bare wire buried under the bracket is the ground from the circuit cable.

They all need to be connected.  The easiest way is to attach a short bare (or green) wire to the green screw and then attach the four ground wires together. 

I prefer the newer push in connectors for solid wires (they can be used for stranded but are a bit harder to use). Or you can use a wire nut. Just be sure to strip enough bare cable to get a good twist on all four wires before putting on an appropriately sized nut. Most practitioners use a lineman's plier to get a good twist on multiple wires.

Never put more than one wire under a screw or nut.