how does surface organic material get so deep underground?
The same way the surface material formed into sedimentary rock.
Do the math, sedimentation as little as 1 inch every 1,000 years is over 6 miles deep after 400 million years.
Oil is found in sedimentary basins that were formed under ancient oceans or lakes. You need to understand that they are only found if rock formation that were formed from sedimentation sources.
The same way it does it now, it settles on the ocean floor and that process has been going on since the beginning of time.