Master Vault is where ALL of your files are stored.
Replica Vault is used at a remote site to maintain local copies of the files from the Master Vault. You need a remote file server for a replica vault. There are rules that can be established as to retrieval and saving locations for the remote workers. You can also control the replication/sync timing.
Cache Vault is the temporary server storage location files when you save. The files are saved to the Cache Vault, then moved/copied to the final master vault folder.
Master Vaults must be established, created, mounted and verified to Windchill, They have a corresponding physical disk location on your system. Could be a local disk or a NAS.
Replica Vaults are only needed if you have remote locations and you have a latency issue. Some companies have remote locations and do not use replica vaults. I have local users (in the same building) and remote users (7 miles away) and I do not use a replica server as we have good fiber optic lines between the sites.
Cache Vault is established OOTB by Windchill. You can move it if you need to.