Always use the online installer if the system you are benching is connected to the internet. It is faster by a lot and you uncheck benchmarks that you don't need and they won't get downloaded.
If you are only benching offline, the offline installer is for you. You will download all currently supported benchmarks, tools and prerequisites, but can decide which ones you really want to install.
The installation will be slower and use more space than the online installer, because all of the installer's compressed data is copied as well to create a local repository. This is necessary to update or change the installation later.
Even if you are benching offline, you can consider BenchMate's portability to transfer your online installation by just copying the BenchMate directory.