You may put scripts for each object in post deployment script like below. Below script re-creates stored procedure with schema [Org]. Hope this helps.
Step1 - Remove Stored procedure added automatically by project since it is created with default schema [dbo].
IF EXISTS (SELECT * FROM sys.objects WHERE object_id = OBJECT_ID(N'[dbo].[spUpdateCompany]') AND type in (N'P', N'PC'))
DROP PROCEDURE [dbo].[spUpdateCompany]
GO
Step2 - Remove stored procedure if already exist in [Org] schema and re-create stored procedure in [Org] schema.
IF EXISTS (SELECT * FROM sys.objects WHERE object_id = OBJECT_ID(N'[Org].[spUpdateCompany]') AND type in (N'P', N'PC'))
DROP PROCEDURE [Org].[spUpdateCompany]
GO
CREATE PROCEDURE [Org].[spUpdateCompany]
@Id int,
@Name [nvarchar](4000)
WITH EXECUTE AS CALLER
AS
EXTERNAL NAME [SQLServerProject.CLR].[StoredProcedures].[spUpdateCompany]
GO