Here is the code as an example,
1. Add the custom user login and user role configurations
    public class IdentityUserLoginConfiguration : EntityTypeConfiguration<IdentityUserLogin>
    {
        public IdentityUserLoginConfiguration()
        {
            HasKey(iul => iul.UserId);
        }
    }
    public class IdentityUserRoleConfiguration : EntityTypeConfiguration<IdentityUserRole>
    {
        public IdentityUserRoleConfiguration()
        {
            HasKey(iur => iur.RoleId);
        }
    }
2. Inherit your custom dbcontext from IdentityDbContext,
    public class CustomDbContext : IdentityDbContext<ApplicationUser>
    { public CustomDbContext() : base("DefaultConnection")
        {
        }
        public DbSet<CustomEntity> Entities { get; set; }
        protected override void OnModelCreating(DbModelBuilder modelBuilder)
        {
            modelBuilder.Conventions.Remove<PluralizingTableNameConvention>();
            modelBuilder.Configurations.Add(new IdentityUserLoginConfiguration());
            modelBuilder.Configurations.Add(new IdentityUserRoleConfiguration());
        }
    }
