I'm probably not the best person to answer this (I've only done like 10 stencils) but I'll try to help. I see two ways you could approach this:
1. Have the deer/pond/frog (everything that's dark in your design) be what is painted, meaning you want freezer paper over all the light green. The spots on the deer would be hard. You could either do "bridges"and paint over the bridge after you take the stencil out, or you could just cut the spots out of freezer paper and iron them on after you iron on the main part (does that make any sense?).
2. Kind of reverse the design--have the dark green be freezer paper and the light green be cut out. You'd need a shape to outline the design in. Basically what it'd look like is a square (or whatever) of ink with a the deer and stuff the color of the bag. Again, I think you'd need two stencils: one with a big square cut out of it and the other the shape of the deer with the little spots cut out. I'm thinking that this would be easier.
SORRY if this is all completely duh or completely incomprehensible. It's hard to work out where you are from your post.
This might help ('scuse my mad paint skillz)