How can I compare records already in the entity against records in an input file?

This will depend on whether your entity is a Basic, ID Matched or Fuzzy. For Basic or ID Matched entities, the ID will be preserved through the Certification Process,so you will be able to use the ID in a SQL statement to look for differences between the data sets  (unless you ask xDM to generate an ID). 

For a Fuzzy entity, the Golden ID is always generated by xDM, so you will need to use either Source Records or Master Records which hold the Publisher ID (Publisher Code) and Source ID.

The answer you're looking for will also depend on what Record Types you're trying to compare. Take a look at the links above, as can be seen in the validation phase of the certification process, you may find  that certain records that are rejected by your data quality constraints (so they won't become golden records) but are still retained in source data as errors.