Drain cherries, reserving the juice (start with 2 jars)
Beat sugar and margarine together until fluffy. Add egg and vanilla and beat until well blended. Add cocoa, baking powder, baking soda, salt and 1/2 cup of flour and mix until well blended. Add remaining flour, mix until well blended.
Shape dough into 1 inch balls and place 2" apart on ungreased baking sheet. If the dough is too sticky to work well (depending on temp in your kitchen), powder your hands with a little flour or cocoa powder, or place dough in refrigerator to firm up a bit before making balls.
When all balls are made, press down in the middle of each cookie with your thumb. (Hint: I've found that the back side of a 1/2 tsp works well for making the space for a cherry) Place a drained cherry in the center of each cookie.
In a small saucepan, combine the chocolate chips and the sweetened condensed milk; heat until chocolate is melted. Remove from heat and stir in 4 teaspoons of the reserved cherry juice.
Spoon the chocolate mixture over each cherry, covering completely. (If the chocolate mixture seems too thick, thin with a bit more cherry juice. It will be thick, but still 'swirlable' to get the best coverage and a nice looking cookie in the end)
Bake at 350 for about 10 minutes. Let sit on cookie sheet for up to a minute, and then remove to wire racks to cool completely.