In the main window of MD5 Checksum Verifier you can see the tabs with th ehelp of which you can Make file MD5, Make check file and Verify Check File 

In the Make Check File tab you can enter a folder for which to check all the files. After the operation is complete the checksum file is being saved in the location that you have specified previously 

Here you can verify the check file. The verifying process will tell you how many files were verified and how many of them were changed