You can slice it and dice it any way you want, really. The constraint is often what data needs to be written within a transaction. You'll have to figure our a way to reliably apply a consistent schema to all these database files somehow and keep track of them.
One of the things I appreciate about SQLite is being able to keep all the schema initialization and upgrades in the application itself, which are then checked into git and can be tested like mad with throw-away copies of the data.
Here's a package in golang I wrote to help with that process:
