Or you could “collapse” some of them down to static meshes, by selecting a bunch together, and from the Details panel, under Brush Settings (click the down arrow first, to expose advanced parameters), there’s a “Create Static Mesh” button.
BSP geometry has its performance overhead, sure (and for prototyping they’re more than all right), but I’m not sure this has anything to do with positioning them…
Here’s something else you could try: copy-paste their values from the Z axis, if you want both of them to share the same height, or, if they have different height dimensions, you could drag both BSP blocks in the air, press the “End” key to snap them to a flat surface, then go into the left/right/front orthographic view and use the Up/Down arrow keys to position them on the Z axis.