Another great question with perhaps a somewhat unsatisfying response.
To directly answer your question, in terms of human ancestors, you're quite right that they're found all over the place and therefore not immediately datable using depth alone. Each find is dated uniquely using a combination of radiometric techniques, knowledge of the geographical area and index fossils. For example, if a lava flow that is dated very accurately falls in the same layers as a fossil which lies ten miles away the continuity of the strata can be used to help date the fossil.
Index fossils are somewhat less applicable to hominid finds, but they are very relevant to counter the claim that fossils are simply placed in order according to presuppositions.
fromhttp://www.enchantedlearning.com/subjects/dinosaurs/glossary/IndexFossils.shtml
* Ammonites were common during the Mesozoic Era (245 to 65 mya), They were not found after the Cretaceous period, as they went extinct during the K-T extinction (65 mya).
* Brachiopods (mollusk-like marine animals) appeared during the Cambrian (540 to 500 mya); some examples still survive.
* Graptolites (widespread colonial marine hemichordates) that lived from the Cambrian period (roughly 540 to 505 million years ago) to the early to mid-Carboniferous (360 to 320 million years ago).
* Nanofossils are microscopic fossils (the remains of calcareous nannoplankton, coccolithophores) from various eras. Nanofossils are very abundant, widely distributed geographically, and time-specific, because of their high evolutionary rates. There are enormous numbers of useful nanofossils, including radiolarians and foraminifera. Nanofossils are the primary method of dating marine sediments.
* Trilobites were common during the Paleozoic Era (540 to 245 mya); about half of the Paleozoic fossils are trilobites. They evolved at the beginning of the Paleozoic Era and went extinct during the late Permian period (248 million years ago).
If an Ammonite is EVER found in an older strata than a Trilobite, the current understanding of evolution would be disproved. There are rare occasions where Plate Tectonics has folded the geologic column but this is very obvious and has been well-documented. You'll never find index fossils out of place without the effects of plate tectonics. Again, this is extremely rare, but when it does happen it's obvious -- if you'd like to discuss a specific occurance you're wondering about, you might start a new thread.
Since these index fossils (and there are literally thousands of them) are never out of order (ever) it leads to the conclusion of evolution not some pseudo-random sorting by a proposed flood. When hominid fossils are found in the same strata as index fossils or even previously dated fossils, it gives a clue as to the date of the fossils.
I'm not a historical anthropological expert, but I'm not aware of any place where major hominid species have been found directly on top of each other. You will NOT, however, find hominid fossils in layers "supposed' to be older than dinosaurs -- such a find would instantly and irrevocably destroy the conclusions of common ancestry if it were shown that there is no geological folding in the region.
