If you already have the excel add-in from your first shop installed, the way to connect a second shop to the same Excel installation is as follows:
1. Open Excel,
2. navigate to the cobby Settings in the Ribbon,
3. Enter the new license key,
4. click Save.
Whenever you want to switch between Magento Servers in cobby, you can now open the settings dialogue and choose the shop you want to point the add-in to.
5. click on the drop-down arrow next to the license-key,
6. click anywhere in the row of the license you want to switch to,
7. hit save and restart excel.
Fast switching between shops only works when both shops are on the same cobby version. If yours aren't already this is a good time to move both servers to the latest version of cobby.