Adding chapters while preserving the original file size and type.

Gone are the days of easily adding chaps in FCP7.  FCPX is here… chapters are gone!.  Now enter Compressor 4. 
When exporting from Compressor am I ultimately going to end up with an additional file with new settings?
I have followed the Compressor manual and understand that I can “Create a new batch from template” and am supposed to choose Create DVD.  I however just want to keep my file in its original maximum resolution while gaining the chapter marks that will be recognized in iDVD or Studio Pro.
Can anybody offer me some advice or point me to some good resources? 

Assume you're referring to Compressor 4, although the following would pretty much also apply to earlier versions.
Yes; you will have an additional file with chapter markers.
Select a preset…you can start with any of them, but Pro Res 422 makes the most sense.
If your source file (the exported Quick Time file) was PR 422, it will not change the scale and will preserve the quality of your original file (or close enough so you wouldn't be able to see the difference even with a blown up projected image). If, for some reason you a codec other than Pro Res, go to the Inspector>Encoder pane>Video Settings>Compression Settings and make your choice. 
In the Preview window, set the chapter markers, which are frame-accurate in an I Frame format like Pro Res.
Submit and Compressor will spit out a high quality QT movie. You can then bring that movie into iDVD, which will recognize your markers.
If you want to use DVDSP, you have two options. 1) You can let DVDSP do the encoding by importing the QT movie with chapters. 2) You can use Compressor to encode; you choose the DVD preset (Disk Burning) and it creates separate audio and video files that you then bring into DVDSP, which will "see" your markers in these files. Most DVDSP users use the second method because they have far greater control over the compression settings…but that presumes the user is relatively familiar with Compressor and Frame Controls.
Finally, bear in mind that DVDs are standard definition, so – however you get there – the DVD will be much more compressed and much smaller resolution than any High Def format. However, the DVD end product can still look very good. Do some tests with small, but representative sections of your movie to see whether iDVD or DVDSP works best for you.
Good luck.
Russ

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