The quantity of Sculptra used is a very individualized decision based upon how much volume in your cheeks you have to begin with. Since most people require three injection sessions, the amount of Sculptra used can be fine-tuned during the second and/or third injection session. Having said that, if only the cheeks are being treated and you want to be conservative, I think one total vial to start with could be appropriate or one vial per cheek if you are starting from a depleted volume state.
What you have is postinflammatory hyperpigmentation due to the skin becoming inflamed in areas of eczema. Chemical peeling is not really beneficial in your situation. A better strategy is to treat the eczema using mild topical steroids for brief periods intermittently to help control the eczema and also using creams such as Elidel or Protopic to also control active eczema. The most specific and reliable way to treat the hyperpigmentation is with a 4% hydroquinone type bleaching cream.
The discoloration usually lasts about 7 days. Bruising in this area is always a possibility, but superficial placement of the Botox helps prevent this.
It is not likely that the Botox itself would be causing your migraines. For those patients who have migraines and have received benefit from Botox, it works very effectively and usually lasts for 4-6 months.