Yes, you can check for duplicates against two objects at once.
To do this you must have a cross-object dataset in Trimmr for these objects. DataGroomr automatically creates a cross-object dataset for "Leads in Contacts". If you need to create others, please see this document.
In Importr module select the Upload > From CSV file.
In the Import wizard, select the CSV file to import by pressing the BROWSE button and add a Title.
Select the target Object in the Import To section.
Note: At this time, you can only import non-duplicates records into one object at a time, but there is a simple way to import them into the second object. You may use the Export feature to export records and rerun the import against that object.
In the Compare To section select your cross-object datasets.
Continue mapping CSV columns and hit Finish, the file will be checked for duplicates against both objects (Leads and Contacts in the sample above).