Hi,
Start with Server 2 and deselect the web tier components.There is no need to go for full installation on server 2.Once you will complete the custom installation on server 2 then you will see tables in CMS and Audit databases.For your landscape you need to select the custom/expand installation on each server.
CMC and BI launchpad will not be accessible until you install the web tier but same time you can see number of BO servers in the CCM for each node.
Amit