As you already know, you can run only one Lync client instance at a time, as with Office Communicator.
Even if the situation is not usual, you may have to use multiple Lync account and off course you can’t use them at the same time.
A friend of mine has shared a tool which allow to manage multiple Lync account (not only which are part of the same Lync environment).
Go to https://greiginsydney.com/profiles-for-lync/ or direct link for download http://gallery.technet.microsoft.com/Profiles-For-Lync-multiple-bef8769f
Don’t forget you can also use Lync to connect to Office Communication Server R2 thanks to few registry settings updates; so this means you can use this tool to connect to both systems
Registry settings to connect Lync client to Office Communication Server R2
Create the following key
Value: 1 (00000001)