If the list contains lots of files that are not checked by default, it is typically because there are lot of orphaned files and you have opted not to delete them. Is that correct?
In that case, you can sort the checklist by an action type (middle column with pictogram). That should group the unchecked (orphan) files.

How do I enable the synchronization checklist option?

After running a Synchronize command I would like to be able to see ONLY those files that are scheduled to be synchronized without having to scroll through the entire list looking for check marks?