Hi Monica,
I'm not sure exactly what information you are after so I'm going to give it a shot and see if this is what you are after.
First off PTGui and Pano2VR are two different types of applications. PTGui will stitch your images together to create a 360 x 180 panoramic equirectangular image as well as providing various export options. Pano2VR on the other hand doesn't actually stitch images but will take that equirectangular image created in PTGui and allow you to define parameters, attach UI skins and export in a number of ways including Flash/HTML using mult-resolution files.
So for PTGui your source files should be of the highest quality and resolution you can shoot. For example I shoot on a Canon 5D Mark 2 with a 15mm Canon Fisheye lens. This gives me a RAW file of approximately 28mb, I shoot 6 around and 1 vertically. When I stitch these in PTGui I'll end up with an equirectangular image around 10,000 x 5,000px.
I use Pano2VR, in conjunction with Photoshop, to do any retouching necessary using the patch tool. Then I create a set of output images, HTML and Javascript files because I incorporate the panoramas using a Web Content overlay (see Bob Bringhurst's excellent DPS Tips app for info on how to implement it). In creating the output I use the option to create multi-resolution files, that provide increased resolution as users zoom in.
Alternatively, if you only want to implement the panoramas via the Panorama overlay, you can use PTGui or Pano2VR simply to export the 6 images. In this case I'd export at around 1,000 x 1,000px in jpg format. If you are targeting higher spec devices you could increase the size.
Tony