To use it, place it into your hotbar and then use the item in the requested area, or use E, , , when activated in your inventory.
The area of effect is quite small, it is not much more than a single foundation.
It does not allow resources to respawn faster, it only allows resources to respawn near foundations assuming the respawn interval of those resources has expired and a nearby foundation blocked their respawn.
Tutorial on how to use Re-Fertilizer, and is it worth it?
Notes
Beware while using Re-Fertilizer, you can regrow a tree or a rock on you and get stuck in it. This might lead to the death of your character, where you would be able to retrieve your inventory on your dead body. It can also lead to the destruction of your body by the anti-meshing system on Official Servers, and as a consequence losing the entirety of your inventory.
The Re-Fertilizer is an almost guaranteed fail in Single Player mode due to the broken respawn mechanics of that mode.