There are two separate files that reference each other. There is no JPEG "in" a RAW file.
I usually don't like to jump in the middle of a conversation, but, I don't know where you heard that with regard to raw files. In many (most) raw formats, there are embedded jpegs for preview. Some cameras offer a raw+jpeg capture capability where two files are stored, but Canons .crw and .cr2 both have a jpeg embedded in the raw file for preview. Some Nikon .nef files (depending on camera) have an embedded preview image that is similar to a jpeg basic.
see here for more raw information:
Raw image format - Wikipedia, the free encyclopedia - scroll down to the file contents section.
For information on the .crw format specifically, this page has a good breakdown:
The Canon RAW (CRW) File Format
scroll down to 0x10b5 which represents a specific location in the crw file that starts the reference area describing the jpeg that is included with the raw data.
Raw files can and many do have embedded jpegs - this is usually the imagery used by portable viewing devices (like the Epson P2000 for example) to display the photo contained in the raw file - those portable devices don't contain near enough processing power to decode and display a full raw file quickly, but they can extract and display the embedded jpeg included with the raw file.
Some cameras allow you to turn off the embedded jpeg format and save the jpeg that would normally be embedded as a separate jpeg file (I believe the 1DMkII has this option and possibly newer in the same line)
What software do I use? Lightroom - why? Because I owned a license key when I switched to Mac, and because other software was more pressing to replace and I liked lightroom, I decided to just move to the Mac version. Eventually I may get Aperture, but there are many things ahead of it on my purchase list