I am getting the error message
"Permission denied (publickey).
lost connection"
when I attempt to do an scp migration. I know how to generate the public keys in both IIS and UNIX, and I believe they are both suppose to have the same public key - but where are they each suppose to be stored (I believe it might be the home directory which I suppose is home/user/.ssh in UNIX but where in IIS?)

In addition, what format should the key be in? (I am not sure if I need to use some "$ ssh-keygen -e -f yourkey.pub > yourkey_ssh2.pub" command to convert the public key to secsh public key file format on the client or just leave it as a long alphanumeric string)? Do the public keys in each server need to be the same format?

Also, Ive read about setting up an "authorized_keys" file and/or an authorization file - but I dont know exactly what these files should contain and where they should be located.

For some background on public/provate key pairs:
Public-key cryptography - Wikipedia, the free encyclopedia

Each ssh server (ie sshd) should have it's own unique host key pairs (ie, nothing to do with the user or your home dir). These verify that the server you are connecting to is who it says it is (via your known_hosts file) and handles the actual data encryption.

Then, each user of ssh can generate a key pair (or many if they wish) if they want to identify themselves via these keys. Whatever you do, don't overwrite one user's generated keys with another just to get a login to work.
To enable passwordless authentication via keys, copy the public key of the source into the authorized_keys file of the destination.

Example:
USER1 on HOSTA wants to be able to log in as USER2 on HOSTB.

1. Log into HOSTA as USER1
2. Generate a key pair for USER1
3. Take a copy of the _public_ key from the pair you just made
4. Log in to HOSTB as USER2
5. Create (or edit) the authorized_keys file (this filename is defined in the sshd configuration on HOSTB)
6. Add your public key for USER1 from HOSTA to the authorized_keys file belonging to USER2 on HOSTB
7. Most key generators create a short comment at the end of the public key, make sure this also gets added to your authorized_keys file (ie just add the whole block) as this makes it easier to manage things if you get a lot of keys. You can make something up in this field if you want to help you track them
8. OPTIONAL: Prepend the key in your authorized_keys file with from="<ip address>" if you want to increase the security by also validating the user by the IP they come from (both must be correct before it will allow a login)