Glad the coordinate issue is fixed. I figured it was that, although there seems to be one in disagreement.
Now with select by location, you know that it makes a selection in the table, If you have added the field already, then you can use the Calculate field to put "yes" in your desired field. The problem then, is you have to switch the selection, which will highlight all the records that weren't within, then calculate again with "No" in the field.
Your workflow is better suited to scripting than a model. However, by using the Results window output, you can export any successful process and see the syntax required.
In any event, there is an option to invert a selection inside the tool process itself
Using Select By Location—Help | ArcGIS for Desktop