In the Compare Schema module, it is not possible to generate one sync script per object or generate the script automatically into specific directories based on object type. For e.g. all table sync script to be placed under table directory, and all views sync script to be placed under views directory.
Submitted to Idea Pond to provide configuration option such that Toad generates one script per object, and groups script of the same object type into one same directory. Please visit the Toad Idea Pond to vote or comment on this enhancement request.