When you save a new preset it should be visible in the list of presets in the Layout or Preset manager. So long as it is in this list you should be able to create a new CSS Sculptor page and select the new preset from the main list. Is this the part that is not working for you? Please explain what you are seeing in the list of presets and any other details about this that you can think of.
For the second main question, no, you will not be able to define where the files are created. You can however after the fact update the reference to the css on the page and move the css where you would like it.
There is no options for inserting text place holders, just what controls you see in the wizard.
Thanks for the suggestions about the positioning and z-index, I have already showed to this to a manager.