The modelstore is your whole application. It has only one version, but it can contained layered elements, just like previous versions of AX. If an optimal deployment with less downtime, you need to prepare a fully compiled and error free modelstore in a staging/test environment. I've blogged about how to deploy the modelstore using PowerShell and a "temporary" modelstore schema here:
yetanotherdynamicsaxblog.blogspot.com/.../deploy-modelstore-with-less-downtime.html
You only install one modelstore in an application database. If you want to have another "version" to compare against, just like you could with "Old" in pre-AX2012, you have the option to install modelstores to the Baseline database. This is however not a requirement for AX2012 to work.
I've blogged about the Baseline database here:
yetanotherdynamicsaxblog.blogspot.com/.../baseline-is-new-old.html
Good luck!