My brakes rotate around after I tighten them and other v-brake questions
Either spacer arrangement is acceptable, and the choice is part of correctly installing the new pads. But I'm not clear exactly what pads you have, as there are two types: one with posts that poke out and bolts at right angles that clamp onto them (older style) and pads with threaded bolts built in that attach directly to the V brake arms.

Typical V brakes should have the arms vertical when the pads contact the rim. The specific requirement is that the pad surfaces are parallel to the rim at that point, and as they wear they will become that way. Those semi-spherical spacers and washers allow you to rotate the pads to achieve that, so you have some tolerance there. That also lets you toe in the pads, BTW.

It's better to have the arms slightly out past vertical with new pads because as they wear the arms will move in. But that should be by a small amount - a couple of millimetres at the adjustment point marked L in the diagram below.

The flat washers shouldn't need to be against the brake pad, normally they're used under the nut to help isolate rotation of the nut from rotation of the pad (so you don't move the pad out of alignment when you're doing up the nut).

 (image from Saccom)