They are in the Application Data portion of your C: drive. You can edit them directly, which I've found to be the easiest method, because if you try to edit them in MC, the application insists on changing some of the values you've already entered.
I don't know whether the settings are worth changing or not. I copied some values I found in a post and used them with some really low-rate encodes of a basketball game (obviously lots of motion). I also changed virttually every setting in the encoder. The resulting encode was pretty darned impressive compared to what I was able to get with the Vegas version of the MC encoder. I can post my settings, if you wish.
[Edit]
I'm now at my main computer. The path is:
C:\Documents and Settings\User Name\Application Data\MCMPEGEnc
where "User Name" is your user name.
The files are stored in files that have the "mef" extension.
You won't have any such file until you actually save one of your own presets. Once you have saved a preset (or copied one that you get from someone else) it will show up as an extra item in the drop down list on the main page. The thing to do is to save the preset, find the file, and then edit it with your matrix values. Also, you can just copy the information in my earlier post into a file, save it in this directory, with the extension MEF and it will show up the next time you run the external MC encoder.
I think there is some confusion regarding that you are talking about the external MC encoder I believe
Oh, if Kanst is talking about the Vegas Mainconept codec, then I apologize. Yes, I am talking about the external, standalone, Mainconcept MPEG codec. I assumed that this was what Kanst was using because I don't think you can do anything with the Quanize Matrix in the version of the MC codec embedded in Vegas.