Take a look at the readme which describes how to add additional paths.
By default, intellij-protobuf-editor uses the project’s configured source roots as protobuf import paths. If this isn’t correct, you can override these paths in Settings > Languages & Frameworks > Protocol Buffers. Uncheck “Configure automatically” and add whichever paths you need. In your case, you’d add .../src/main/java/proto (where ... means whatever your project’s base path is).