I think the casting is feeding the thick ingate on the center cavity and that is why it is the only one showing shrink at the top. By moving it to the cope side and moving the sprue closer the sprue will feed the ingate and cavity. If you use a sprue well at the bottom I would make it as little as possible to avoid feeding metal from the sprue and ingate to the well. I would add a 1/4" vent hole in the thick sections if you are concerned about them shrinking. The vent will not only let some heat out and give you better surface finish but will feed the thicker sections if you make the contact point heavy enough.