Their is nothing wrong with the dual graphics card, except linux does not yet support the dual graphics feature. hopefully in the near future it will support dual graphics.
I leave my laptop in Ati mode unless I know I am going to be useing it for extended time on the battery, then I switch it over to the Intel. (I can get almost 5 hours batterylife in kubuntu in intel mode combined with intel powertop)
whether linux effects the backup/recovery partition is all in how you partition your HD. I would very stronly recomend making the backup dvds, this way no matter what happens you are safe.