Not knowing what ALL components are in the kit you purchased, the plastic bag could contain parts for any number of tapered stud positions in the steering system--idler arm, tie rod, or center link.
As far as the center link, you have 2 different methods of securing the tapered studs--castellated nut and cotter pin, or self-locking nut. Part of the problem is getting the tapered stud(s) properly seated before you could replace a regular/castellated nut with a self-locking variety. The seals should go wherever the seem to fit best, and I do agree it is confusing what the makers of these parts do when packaging the parts with little useful or specific instructions on what is to be done and/or why it has to be done a certain specific way.
I don't see any lube (zerk) fittings on that center link or in the parts layout in the picture. They are essential, so find some and install them if they aren't there already.