Permissioned blockchains on EVM: are these private ledgers os it all on ETH main net? Private blockchains using EVM: is this really the equivalent of the library of tools in hyper ledger or do these blockchains run on the public main net?
They are completely separate networks, with a different genesis block.

Geth and parity support running your own private networks that can utilize the features of ethereum (and the ecosystem of tools for it), without having to interact with the public network.