See "Running a plugin in Chrome": http://www.chromium.org/developers/design-documents/pepper-plugin-implementation You need to use the --register-pepper-plugins command-line flag.
Note that:
- Running .dll plugins is not a supported way to ship to Chrome users. It's fine for testing, but to ship your plugin to users, you need to use the NaCl or PNaCl toolchain.
- It doesn't really make sense to put your .dll file with the server. The server has no use for it; it's only for use by Chrome. There's no viable way to make Chrome download a .dll and load it; it needs to be available to Chrome at the time that you start up.