I deploy from source, with several custom modules, and my typical workflow is the following:
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During app development, I download the latest mojoPortal code with TortoiseHG each time before I launch Visual Studio.
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I test builds on my local workstation (configured to run IIS), and build/publish/clean/backup target/upload to our development server if I need some collaboration from others for testing.
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When a new version of mojoPortal is released, I usually wait a couple of days to see if problems are reported, then notify our webmasters that I am updating the production server. I then download the latest source with TortoiseHG, and build/publish/clean/backup target/upload to both development and production servers. If a problem is identified after I have deployed to production, I run this sequence again once it's fixed in mojoPortal or my own code.
I hope that helps.
Jamie