I have an application using EF as ORM. The database used to have one schema, dbo and everything was working fine. I recently organized my tables into 4 different schemas. So
You can map each table to its own schema by fluent mapping only. In your DbContext subtype you should override OnModelCreating (if you haven't done so already) and add statements like this:
modelBuilder.Entity()
.ToTable("t_Department", "school");
Entities that you don't map like this explicitly will be placed in the default dbo schema, or you can provide your own default by
modelBuilder.HasDefaultSchema("sales");
(summarized from here)