By "copy & paste" do you mean FTP? By "each part of the website", do you mean each individual site?
In multisite, you only have one set of plugins (located in wp-content/plugins), that are then accessible for each site. This is one of the advantages of multisite, that you only have one set of plugins to keep updated. Even if only one sub-site uses a plugin, it still gets installed & potentially available to the whole network.
To make a plugin active on all the sites, "network activate" it as Ipstenu suggested. This will still mean that each plugin can have individual settings within each site.
If you want to manage all the settings centrally, then use the plugin suggested.