How should I ground two switches in a handy box that were previously ungrounded?
All the ground wires in a box should be connected together, so add a pigtail from each switch to the ground wire nut, and connect them all together.  If this gets to be a lot of wires (sounds like 3 cables and 2 switches, so 5 total) it may be easier to use a push-in connector instead:



or for 6 conductors: