Nearly every issue users have with low confirmed link numbers is due to bad proxy setup so if you do not have your own proxies or a tool to find good working proxies that are checked against the search provider you wish to use then leave it set as default.
This is a very simple and quick process, if you are installing NHSEO for the first time it should be enabled by default. All you need to do is go to the Settings => Proxy tab:
In this tab you only need to have two options enabled, highlighted by the blue squares, "Use Proxies" in the proxies for searching controls and "Use Proxy Harvester".
When you have enabled these options hit Save and you are done.
As for the other settings I strongly urge you not to change these, the default settings for all options are set that way such that they are appropriate for the majority of users and as such do not need your attention.