Concept: using 2 databases in one project or how to separate migrations

Hi folks

just a question of concept about using 2 databases for the same
Situation: running a project which uses a plugin with its own database
structure, migrations and initial data loads, now I want to extend the
functionality of this plugin using my own models, db objects,
migrations etc. in addition to the objects coming with the plugin.
Running this in one db will give you problems regarding the migrations
My question: is it better to run 2 dbs to separate the different db
models or is there a way to have seperate migrations?