1. Deployment
For deployment you can use the built-in MSI generation wizard.
It means you deploy the application on a dev environment using Visual Studio, then on the admin console, export the application a MSI using the wizard.
Finally you can use that MSI to deploy the app to the Production server.
That's a two step process (Run MSI, import MSI in Bizalk Admin console).
Note that only your Biztalk assemblies are installed by the MSI.
If you use .NET assemblies in your solution, they need to be GAC'ed manually.
You will also need to restart the host instances running your Biztalk application.
See details here:
https://msdn.microsoft.com/en-ca/library/aa559168.aspx
That's a few manual steps.
Alternatively you can automate some of these steps by using the BTSTask, a command line tool included with Biztalk.
You can script all the manual steps.
Obviously it takes time to write such script, so it's only worth it if you are going to deploy many times in non-dev environments.
BTSTask reference:
https://msdn.microsoft.com/en-ca/library/aa559686.aspx
2. Redeployment
Usually you completely remove the old version and then install the new one:
Delete the application from the Biztalk Administration Console and ungac the assemblies it uses.
The whole process would look like:
1. Make sure there are no running instances in you application. You can always disable your receive location and let the running instances complete
2. Delete Biztalk application
3. UnGAC associated assemblies
4. Deploy new Biztalk application version and GAC associated assemblies
5. Restart Host Instances used by your Biztalk application
EDIT: To address OP's concern about deleting a running application:
It is indeed possible to deploy resources independently and never delete your application.
But it does not mean you will not interrupt the service.
An orchestration for example, can never be redeployed when it has running instances.
So assuming that you divided your functionality properly into applications, I find it cleaner and easier to delete the whole application than going after each resource.
Otherwise, yes you can go and replace your resources separately.
But to me it seems like an overhead caused by not having defined applications correctly.
3. BTDF
The Biztalk Deployment Framework is a good tool to have some kind of automation in your deployment without having to write the scripts yourself.
Good compromise between customization to your needs and setup time.
I have used it on a freelance project. It was very helpful because I was able to deliver a package with a only a couple of deployment instructions, and the non-techie client was able to deploy painlessly.