I don’t think you have explained your problem space
Putty and WinSCP are SFTP clients. They will transfer the certificates for you but they will not install them
Can I confirm a couple of things
A) Are you trying to use a windows based client to generate the certificates and then install them on a Linux Machine
B) It is possible to upload the certificates to a folder eg /etc/mycerts and have a web browsers to point to those certificates
C) Apache needs a restart after you upload the certificates - how are you planning to do that?
While technically what you are describing is possible you are trying to use tools that are designed to move files to do more than that
As an aside - SFTP is a subset of SSH and most SFTP sessions for security reasons do not allow an interactive shell (i.e. let you run commands like service restart)