To use the plugin you will need to expand the Protowire panel in the bottom right of Sketch by pressing the grey arrow next to the Protowire logo. When you've finished prototyping you can collapse the panel which will hide all the links so you can concentrate on designing.
The artboards of the prototype have to be on the same page i.e. a prototype can't span multiple pages, though you can have links in the Symbols page that link to your prototype.