I’m building a wooded deck about 16 X 32 feet that will be about 2
feet off the ground.  I live on the side of a hill and all of the
ground under the deck is solid limestone. There is about 3 to 5 inches
of top soil on top of the limestone.   I need to know what my options
are to install the concrete footings for the deck and how to do it. I
also need to know my options on setting a fence post in limestone.

You might have to get into a rock anchor system:

http://www.williamsform.com/Ground_Anchors/ground_anchors.html

which gets into drilling into the rock and setting threaded
rebar or similar anchoring material.

Once the anchors are set, you can then pour footings or place
post supports, etc.

Unless you are building to last a century, or the slope exceeds 10%,
my guess is you can use twice as many pillers as usual, in slightly
over size holes, as shallow as three inches if that is as deep as you
can make them without extreme effort. Fillthe holes half full of weter
than usual sackcreate or equivelent. Finnish filling the holes with
sacrete with the normal amount of water. Borring into the lime rock is
better, but I think quite costly.  Neil

If you can change the fence direction a few degrees at each post so
the fence makes a quarter of a circle or more, it will be quite strong
inspite of shallow footing of the posts. Perhapsyou can follow
approximately one of the contour elevation lines so you don'thave to
stair step your fenceat most of the posts. You can put most of the
fence sections several inches off the ground, level at the top and use
one by twos or one by fours or one by six boards to fill in at the
bottom. It doesn't look as tacky as you might think and a single board
is easier and cheaper to replace than a whole fence section that
rotted out at the bottom.  Neil