1)Setup User in Access Control ( Local or AD ) 

2) Make sure Auth with Cert is ticked

Setup Virtual Folder and set to home

Get end user to create a new Public and Private Keypair 

https://www.ssh.com/academy/ssh/putty/windows/puttygen ( RSA ) 

Get end user to share Public Key with you ( they keep private key ) 

Copy  their Public Key 

Sits in C:\Program Files\VanDyke Software\VShell\PublicKey\%username% called Identity.pub

Top line should be 

—- BEGIN SSH2 PUBLIC KEY —-

User should then auth to server with .ppk file using SFTP client like Filezilla