Yeah, you can restore using the All apps + data option. Or if you want fewer chances for conflicts depending on how radical of a change you jut made with the Rom flash, you can single out certain apps (such as HTC Sense or Launcher Pro) and restore apps and settings to only those while restoring just apps only elsewhere.
Example:
Open Titanium > Menu > Batch > Restore All Apps With Data > Deselect All > Reselect only Launcher Pro > Click App + Data dot > Click Run the batch operation
Now you should not only get Launcher Pro back, but also your last used configuration on all home screens. If you're just flashing an update to a Rom you're already running, just do app + data for the whole works and everything should be the same.