The bottom board (assuming you are running them horizontally between posts) will need the most thorough treatment, because it will be wettest during rain, and damp most of the time where it is close to, or touching, soil or foliage.
The topmost surface as well because it has no protection from rainfall.
Fences are mostly made of very thin timber which doesn't rot much, its thinness means that it dries out as soon as the sun shines on it, and during rainfall it is thoroughly wet, so there is hardly any time when it has the slight dampness that promotes rot. However your scaffold boards are thick enough that they will be slow to dry out.
Most fence treatments leave a waxy water-repellent film, but for anti-rot and insect preservation, you need poisonous chemicals. The spirit-based treatments penetrate better than water-based. You can stand the ends of the boards in a bucketful so it soaks into the end-grain, and apply several flowing coats by brush onto other surfaces. If you stack the boards (or lay them in a plastic-lined trough) any run-off or drips will not be wasted.
You really need to treat the boards before fixing, when you can do all surfaces.
I've taken to this sort of thing:
https://www.wickes.co.uk/Wickes-High-Performance-Exterior-Preserver---Woodland-Green-5L/p/170778
https://www.wickes.co.uk/Ronseal-Total-Wood-Preserver-Clear-5L/p/164254
https://www.wickes.co.uk/Ronseal-Multi-Purpose-Wood-Treatment---5L/p/147142
https://www.wickes.co.uk/Wickes-Shed+Fence-Preserver-Red-Cedar-5L/p/170774 (on clearance)
Also the Cuprinol products.
The outdoor ones usually contain a decorative colour (keep stirring or shaking as it sinks in the can) and a water-repellent. Clear ones are sometimes intended for interior woodwork that will be stained or varnished, and not exposed to the weather. Outdoor ones may smell somewhat while the solvent evaporates.
older builders will remember Cuprinol Green wood preserver. The original seems to be discontinued, probably because it was too poisonous.
If you look at the labels and the data sheets, you will usually find that they contain an insecticide (for wood-borers) and a fungicide (for rot). Chemicals that are not water-soluble will resist being washed away, once dry.
If you are using wooden fence-posts, they will certainly rot. Stand both ends in a bucket of preserver. The worst rot will be just about ground level, where the wetness from the ground meets the air from above, and gives ideal conditions for fungus to grow.
Concrete posts, or spurs, do not rot. You will appreciate this more when you do your
second fence.
