The i1Publish will not work with the built in spectrometer. So you will have to print out out your test chart and measure it manually with an i1Pro or the new i1Pro2.
I cannot speak for the i1Pro2, but with the i1Pro1, you get a rinky 12" plastic guide that tends to move all over the place. You need to start the scan of each line at aspecific point, and move it at relatively stable pace until you get to the end of the line of patches. Then you repeat for each line of patches. The software will confirm whether or not it was a valid scan. With APS i typically use large 918 patchset. I don't have the patience to do this with the i1Pro handheld.
It would have been ideal, if i1Publish (the softwaer from xrite) supported the builtin-spectrometer in the printer, in which case the scanning would be automatic. It is their OEM (or one of their acquisitions). They claimed that the version in the HP was rigged specifically for HP and would only work with APS (also rigged x-rite software, but not supported by them).
So if you want automated scanning of patches, you need to buy the rather pricey robotic arm thingy, at which point you may as well outsource the gjob to an expert like Digital Dog.
In my case, I am really starting to like IP 9 with my Epson 3880. Profiles look very good, and are well matched to my monitor.
Other issues have also soured my experience with HP. CS6 soft proofing is a real downer. The prints don't look half as bad for gamut/contrast/color as the softproofer will lead you to believe. Also, recent OSX 10.8 permissions totally wonked out all my profiles. So again, IP has been a no nonsense solution so far, and when I have had to call them for support, it's been very good.
The new 9900 also has some cool features like cutting canvas, and front loading of roles. THe 350ml carts also seem like a good idea, although I would likely never need the 700ml ones.
I am going keep my current setup for the next few months, as the HP appears to have entered its manic phase, and when it works, well, the prints are beautiful. In the meantime, there may be some new products from Epson.