The Picture Controls don't affect raw images processed with those programs or most raw converters. The one thing that you might just want to be aware of is that they will affect the jpeg preview you see on the LCD screen and more importantly, the histogram. A contrasty, vivid Picture Control setting will give you a less accurate view of channel clipping (and make both it and the "blinkies" more conservative). If you want to increase the accuracy of what the histogram is showing, go with a Neutral setting and dial down the contrast. If you want to get fancy, you can also do things with the white balance, but that's something that requires a bit more work to recover from in post-processing.