Starting with version 2012.1, after you have made choices on the 'Wizard' screen and click the Next button, Pathagoras will ask if you want to save the selections. If you think you will reuse these choices (either in case you have to remake the current document or if you are likely to create new documents with the same values), say 'Yes'. Provide a record name when prompted. (This is similar to the Instant Database used to record personal values that will replace variables. Pathagoras will record your choices for later use and then proceed to implement your selections.)
If a second or subsequent screen of the Wizard appears, Pathagoras will automatically record the choices in the same file named in the initial screen. Pathagoras will make all changes to your document (making Options choices, deleting optional text you elected not to keep, repeating text blocks and incrementing variables as appropriate, etc.) as reflected in your selections.