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You need to position a targeting point for your spells. Usually this is a gnome. The gnome should be placed in the middle of the garden on the ground. Since your plot is already constructed, you might need to remove one plot in the middle of the garden to properly place the gnome on the ground.

Once the gnome is placed, when you cast your large spell, point it at the gnome. Center the big circle on the gnome. If you do it right, then the spell will include the 3 layers of the triple stack garden.

If you have more than 3 layers or are using the triple seed planters, a different strategy is needed but the above will work with just a triple high soil garden if they are only 1 crate apart from each layer.

Lem27 on May 8, 2020 wrote:

I just made a triple stack 42 plot garden for my couch potatoes, but the ones on the top layer won’t get the effects of a music spell or any area spell. The only way I can deal with the needs right now is by doing them indovidually, but that takes a ton of energy and there’s still no way I can deal with pests. How do I fix this?

I've heard that if you construct your garden so that you can target the spell on the level of the middle patch, then it will affect all three layers. Try doing that.

You have to activate the spells on the middle layer of soil plots. By doing that, it will also cover the layer above and the layer below, thus covering all three layers.

You can do that by putting some object like a crate, a pole, or something that goes up vertically a little bit (ideally something taking up only a small bit of ground space). It should be placed in the middle of the soil plot group. Then when you're about to activate the spell, move the cursor up the object by mousing over it. Be sure you're on that object and NOT on a plant in front of it. The ring of coverage of the area of effect spell will center both horizontally and vertically on the mouse pointer position in X,Y, and Z coordinates. When the coverage ring intersects the middle tier of soil plots properly, you will see it sort of partially highlights them in the horizontal plane of the ring.

Before you activate the spell, walk around your garden plot to make sure the coverage ring covers all plots (any given plot must be at least more than half covered by the ring). Then activate the spell and it should work.

Remember that precise pixel spot that you activated on, and then repeat for the other spells and again any time you come back to tend to garden needs.

P.S. You're question would be better fitted to the gardening message board section, as your question does not actually refer to a bug in the game.