Actually, this should be a non-issue. Starting in Visual Studio 2012, there's an option to set the Schema for the T-SQL wrapper objects. In the project properties, go to the "Project Settings" tab, and on the right side, under the "General" section, there is a text field labeled: "Default schema". That is the Schema used for the T-SQL wrapper objects (I don't usually use the SSDT deployment so I just reconfirmed this info in Visual Studio 2015 — I know, I know, I really need to update).
This was also mentioned in my answer to: Schema for CLR Stored Procedure During Deployment
If the version of Visual Studio / SSDT you are using does not have the option to set the Schema OR if you need to place the objects into multiple Schemas, then you should be able to simply add a T-SQL post-deployment script that moves the objects to the desired schema. By adding a T-SQL script and setting the properties to "post deployment" (or something similar to that), it will get inserted at the end of the generated publish script.
If it's only a small number of objects that won't really have new objects introduced, you can do explicit statements for each object:
ALTER SCHEMA [foo] TRANSFER [dbo].[MyProc];
If it's a large number of objects and/or new objects will be added occasionally and you don't want to deal with remembering to add them to this post-deployment include script, you can cycle through the list of objects that are associated with that assembly to create a Dynamic SQL script that can move them all without anything but the Assembly name being hard-coded (and technically that might even be able to be dynamic using MSBuild / SSDT variables):
DECLARE @SQL NVARCHAR(MAX) = N'';
SELECT @SQL += N'ALTER SCHEMA [foo] TRANSFER [dbo].'
+ QUOTENAME(obj.[name]) + N';' + NCHAR(0x0D) + NCHAR(0x0A)
FROM sys.assembly_modules amd
INNER JOIN sys.assemblies asm
ON asm.[assembly_id] = amd.[assembly_id]
INNER JOIN sys.objects obj
ON obj.[object_id] = amd.[object_id]
WHERE asm.[name] = N'Company.Area.Technology.ProjectName' -- do not use [ and ] here
AND SCHEMA_NAME(obj.[schema_id]) = N'dbo'
PRINT @SQL; -- DEBUG (else, comment out)
EXEC (@SQL);