Select Tools > Options and click the Workbench icon.
Automatically save workspace before running: Automatically saves your .fmw file after a translation, using a default name based on your source and destination formats.
Open up attributes when linking transformers: By default, feature types are expanded to display attributes whenever a link is established.
Draw bookmarks with a filled background: Bookmarks are shaded instead of transparent.
Show unexpected input dialog: An important part of FME is being able to choose not to read certain source feature types; this can be done by removing them from the workspace. For example, if you don't want to read a certain layer in your data, you would delete the applicable feature type. The Unexpected Input Remover (UIR) is that function that discards such data. It checks the input data against the structure (or schema) defined in the Workbench or mapping file. If the data doesn't have a matching feature type, it is discarded. The results of the UIR are noted in the log pane, in two separate places. This checkbox allows you to optionally display the information in a dialog box. See this FMEPEDIA article for more information on the UIR.
Allow source feature type editing: This feature, which is unchecked by default, allows you to edit the definition of a source file.
Enable quick connect: To connect elements of a workspace, you can enable this feature to click an output port, release the mouse button, and then click an input port. This provides an easy alternative to the "drag and connect" method.
Automatically generate header annotations: New workspaces will appear with the default Source Types, Data Flow, and Destination Types annotations that appear at the top of the workspace.
Use transparent annotations: Gives annotations a transparent background.
Automatically create summary annotation: Summary annotations display detailed information on feature types or transformers.
Save recovery data: Specify whether (and how often) you want Workbench to write a recovery file for your workspace.