How to update Geofield using a custom form and DrupalGap's node_save?
From this example it looks like the syntax is along these lines:

var node = {
  type:"donation",
  title:"Donation",
  field_donation_amount: {
    und: {
      0: {
        value: form_state.values.amount,
      },
    },
  },
};


Addition:

So have you looked at something like this then?  Nesting things further, eg:

var node = {
  field_geocoordinates: {
    und: {
         0: {
            geom: {
                  lat: FOO,
            },
         },
    },
  },
};


(I think I have the correct number of }s :)  Perhaps a js version of php's print_r (here is an example) of a valid node object from node_load() would help out?