Firstly, you should use the new GOP developed recently, it's 1-12-2-1-24 for both PAL and NTSC. Also uncheck 'detect scene change' as it's currently recommended. You'll have to use the new file size prediction formula which you'll find in the prediction forum.
The GOP settings stay the way they were the last time you used the program. They will only change if you load a template that has a different GOP or if you change the values manually. I never load any templates as I enter all the changes manually so I don't have to touch the GOP settings unless Kwag comes up with an optimization once more
What comes to the second question, I'm not sure. However I think that the source aspect ratio really doesn't matter as you won't be resizing in TMPGEnc, you're doing that in the Avisynth script. Personally I would leave the field as it is after you load the script in TMPGEnc and select 'full screen' as the arrange method. This is what I've used. You'll see if it's all wrong when the preview is shown while encoding.
The sample and the final encode should naturally have the same settings.