RAW is sensor data. It does not contain any post-exposure adjustments or edits. Any file that has any post-exposure edits or adjustments is not, and cannot be, RAW.
"DPP edited RAW files" simply cannot exist. Once the RAW data has been converted to a viewable image file format, it is no longer RAW. In order for you edits to these files to be saved, your software must create a new file. This file cannot be RAW.
Every use of a RAW converter produces an image format file. You select the image file format (e.g.: JPEG, TIFF). These image-format files can contain edits and adjustments. RAW files cannot.
A practical workflow using Aperture would be to use DPP for conversion and any edits you want to make, then export from DPP as 16-bit TIFF, and import the TIFFs into Aperture for storage and any other adjustments you want to make. The path through DPP is one-way, though: after you have created the TIFFs, you can't go back to DPP and change them.
DPP writes the changes in the RAW file metadata. Because it's Canon's own software, it's the only one that can actually alter the metadata of the RAW file. Aperture stores edits in it's own database, as do all the other RAW converters (LR, DxO, etc.). For the other programs, you can export a sidecar file that contains the edits (altnough only the same software will be able to read the sidecar file).
Bottom line, you can safely edit the same RAW file with both DPP and Aperture, as many times as you want - each is independently nondestructive, and each will maintain it's own record of the edits, but neither will see the other's edits. If you want to successively edit the file with both programs while maintaining full bit depth, you'll need to convert it to a 16-bit TIFF image in one application, and import that into the other editor.
As I understand things, it's a mistake to think that you are ever actually editing the RAW file. A raw file does not contain an image, it contains camera sensor data that can be processed (rendered) to create an image.
A raw file contains an image just as does a TIFF. The raw image contains data in a mosiac format, whereas the TIFF uses a separate channel for each of the RGB components. Shown below is a straight dump of a raw image as shown by Rawnalize--it looks to me like an image. However, it needs to be demosiaced by a raw converter just as the three separate channels of a TIFF need to be combined in Photoshop.
DNG is rendered (demosaiced) data. So no, you are not sending the actual raw data from DxO to LR in the same way as simply using the original data (or converted DNG) in LR. Keep in mind that a DNG can contain rendered data. No different from a TIFF.
DNG files produced b DxO Optics Pro are not really Raw files as the ones that come out of the camera. First, they have been interpolated and demosaiced, since that's the only way for DxO to apply the optical corrections.
These DNGs still are not completely rendered files, that's why they open in ACR. Compared to Tiff's, they are not color space encoded nor gamma corrected.
However, those files have not been color space encoded. When you open them in LR/ACR, you could still select a camera profile and white balance as in a Raw file.
An important note is the way blown out highlights are treated when using this workflow: the resulting DNG don't have those highlight at saturation (equivalent to 255 in 8 bits) meaning that if you perform white balance in LR/ACR and then apply highlight recovery, your highlights may result non neutral. In this case you should perform white balance in DxO before producing the DNG.
Storing images as TIFF files is very space inefficient compared with raw, as TIFF images store three colours per pixel (at 8 or 16 bits per colour component, 24 or 48 total) compared to raw which just has the monochrome sensor data at 12 or 14 bits per pixel total. This monochrome data is interpolated into colour by exploiting the RGB colour filters placed in an alternating pattern over each pixel. To store the full range of colours available in the Raw you would need a 48bpp TIFF, which would take up about three times as much space (before compression).
Also raw preserves the maximum amount of editing flexibility - you're not commiting to any particular white balance or noise reduction setting. TIFFs are better than lossy JPEG images for archival purposes, but still not as good as raw.
I always keep the original Raw files, and keep a matching set of high quality JPEGs for easy viewing. There are arguments for using TIFF for archival purposes as it's an older, better documented format, understood by a much wider range of software. However if you're concerned about future compatibility then you can losslessly convert your proprietary Raw format images to Adobe Digital Negative files, which is an open format more likely to be supported in the future. The redundancy in an uncompressed 48bpp TIFF will make it slightly more tolerant of data errors, however. As Reid states there are better ways to guard against data loss, such as a backup system with error correcting codes, mirrored RAIDs etc.
I am now realizing the power of RAW for easy whitebalance and using Canon's DPP for DLO, and lens corrections. Also I do not want to spend hours working on RAW files and I like the "Canon Picture Styles" that come with DPP, which will likely be enough for 90% of my pictures.
So my question is, what and how should I manage my workflow?
I am thinking:
1. Copy RAW pics from SD to harddrive RAW directory;
2. Use DPP to sort through them and rate and discard;
3. The ones I keep, apply Canon Picture Style, work on whitebalance, sharpening, DLO, Lens correction etc. if needed;
4. Export all into TIFF to Aperture;
5. Do any further adjustments in Aperture if needed, including TOPAZ DeNoise plugin;
6. Export from Aperture as JPG into iPhoto;
7. Delete TIFF files from Aperture and re-import jpg into Aperture and organize (mainly to save space since TIFF files are huge).
(Yes this will work; the essential step is #4, making a tif, because, as you apparently realize, there is no other way to carry DPP edits over to Aperture. But perhaps you should reconsider whether you really need DPP. The only DPP editing that Aperture can't emulate or at least approximate is DLO which is a great tool but also has its downsides - it doubles the size of the CR2 file and, as said before, requires the creation of the tif. Personally, I have decided to forget about it for every shot except those destined for large prints where sharpness is more critical. I use LR, but like LR (and DPP, for that matter) Raw images edited entirely in Aperture do not need to be routinely converted to jpgs, only when one is needed for a specific purpose and it can be deleted afterwards.)