That's an easy question to answer. The answer is, "you're quite mistaken about petroleum only being found deep, and there are many mechanisms by which biogenerated petroleum can end up in so-called 'basement reservoirs'".
Where did you get these fallacies -- creationist tracts, or anti-oil-industry conspiracy sites?
The world's first successful drilled oil well was the Drake well in Titusville Pennsylvania, in 1859. It struck oil at the depth of a whopping 69.5 feet. That's not a typo.
Drake chose this area because people had been striking oil accidentally while digging water wells.
I'm sorry, did I hear you say that petroleum is only found at depths of thousands of feet?
Sure, most modern wells are typically thousands of feet deep, but only because a) we're able to drill that deep now with high-tech equipment, and b) the "easier" shallower fields have mostly already been drilled and drained over the past 140+ years.
Here's a depth distribution of US oil-producing formations:
As for "below the fossil record", note that life existed on Earth long before it developed hard body parts (like shells) which would readily fossilize. "Below the fossil record" is not synonymous with "below the point where there was life".
But in any case, there are known ways by which biogenic petroleum can end up in basement rock, including:
There are many possible sources for the oil accumulations in basement reservoirs, however, three sources are referenced most commonly:
- Overlying organic rock from which the oil was expelled downward during compaction.
- Lateral, off-the-basement but topographically lower, organic rock from which oil was squeezed into an underlying carrier bed through which it migrated updip into the basement rock.
- Lower, lateral reservoirs from which earlier trapped oil was spilled due to tilting or overfilling (Landes et al, 1960).
Mechanisms have been identified that could allow the downward migration of oil into fractured basement when fracture dilation is caused during shearing in an anisotropic stress field (Pine & Batchelor, 1984). Dilatancy in the underlying reservoir rock reduces hydrostatic pressures in local areas of deformation. Pressure gradients are thereby established between the potential basement reservoir rocks and the overlying source and carrier beds containing oil, gas and water. Thus, a tendency to 'suck in' fluids into the basement rocks will be created; this view is supported by direct observation, McNaughton (1953) and McNaughton & Garb (1975).
-- from Hydrocarbon Production From Fractured Basement Reservoirs