I typically handle this by using a post-build copy command (using Build Events, so they're automatic) that puts the dependency assemblies into a shared folder.
I then make sure this folder is included in my IoC container's search path, so they get found.
Another, similar option, is to use a build event on your main application project. It can then copy the dependencies into an appropriate folder. This has the advantage of allowing different dependencies to be used for different applications within the same solution, while still being easy to maintain.
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