This answer assumes you're working in the Part Design workbench.
So you want to adjust the starting height of a pad or pocket. There are two ways I can think of to do this easily.
Adjust the Z attachment value of the sketch to lower the sketch below the surface.
Use the "two dimensions" option in the pad/pocket operation and set the second value ...
I am sorry to tell you that SketchUp is not a good software for printable 3D designs due to its exporting feature not properly reducing complexity. It creates unnecessary faces and vertices inside of items on a regular basis, which in the slicer creates artifacts.
To make a SketchUp created file well printable, a huge amount of careful re-engineering in a ...
I would like a better answer involving automatic alignment, but this was my solution.
Make the object a single component.
Make sure the guide points are accurately located.
Cut and copy the first component to the origin.
Copy the component to the guide points.
What also worked better was to break the grouping of components into building blocks that could ...