Now and after having the Lync-Skype Connectivity officially released, you can download the Provisioning Guide for Lync-Skype Connectivity at this location.
few things to note. in order to make lync-skype connectivity available, if your organization is already provisioned for MSN
1 - You don't have to reprovision or initiate a provisioning request for skype so you can skip the provisioning part and jump directly to the Lync Server configuration, which consists of the following.
1 - Remove the existing Public Provider for Messenger
Remove-CsPublicProvider -Identity Messenger
2 - add a New Public Provider for Skype
New-CsPublicProvider -Identity Skype -ProxyFqdn federation.messenger.msn.com -IconUrl "https://images.edge.messenger.live.com/Messenger_16x16.png" -VerificationLevel 2 -Enabled 1
you will notice that the Proxy Server and even the icon URL for the Messenger and skype providers are the same, however they have verification levels.
once the Server configuration changes are applied, Lync users can start adding skype users to their contact list using skype MSA accounts which means skype users must sign in to skype with a Microsoft account formely known by Windows Live ID in order to communicate with Lync contacts.