In a recent project, I had to find out which of the workflows in the site collection were made with SharePoint Designer. I did a recursive code that checked in all SPList instances in every SPWeb for the following combination:
For each SPList.WorkflowAssociations
SPWorkflowAssociation.BaseTemplate == null
I also checked to see if the workflow association was active (SPWorkflowAssociation.Enabled == true) because the previous versions of the SPD workflows are also stored as associations, but they are disabled.
I hope this little snippet can help you in similar cases. Have a nice coding!