If I am going to use the chart feature in DNG PE to make my own profile, is it better to convert my Raw Canon file to the DNG format through the DNG converter or through adobe camera raw using the save feature. What changes made in ACR will be "stored" in the DNG file? Which way to go?

Doesn't matter. Both will work equally well.

All of your edits made in ACR will be stored in the DNG (as metadata; the original image data is not touched).

It doesn't matter what edits you made, however, since those edits aren't taken into account when the PE builds a profile from the Chart Wizard.

See here for more info, under "Apply Camera Raw Adjustments"

<http://labs.adobe.com/wiki/index.php/DNG_Profiles>:Editor#options_menu

Good to know. Thanks