Groups will gather in the topmost layer.
To keep the objects in different Layers, you may use Select>Save Selection, give it a name, and work with it through that name in the Select dropdown.
In either case, select all, across the Layers, to start with.
i'd like to use the logo, which contains different elements on separate layers, as one unit to apply an effect to the whole logo (a warp transform). how should i do that?
If you must keep the Layers as defined, make them all sub-Layers of a parent Layer. Then target the parent Layer and apply the Warp Effect to the parent Layer.
Understand, even using this method, the Layers/objects involved still have to be contiguous in the stacking order. You cannot Group or Layer non-contiguous items from within a stacking order.