Hi Jodi,
When I started Accutane my skin was pretty bad. Not cystic but just continuous break outs. My initial break out with accutane wasn't bad at all, come to think of it, I don't think I had much of an initial break out. I started with 20mg a day and ended up finishing it on 60mg a day. I started seeing really good results around the second month. I had such minimal side effects I didn't even feel like I was taking anything.
You can read about probiotics at therawworld.com, I take Primal Defense by the Garden of Life brand because I know they are one of the purest forms. One thing that probiotics do is help restore the good bacteria, they also devour undigested matter, and eliminate yeast, parasites and bad bacteria from the intestines. There are so many positive things probiotics do. I order mine from that site I mentioned but you can also purchase them from a health food store.
Also, are you using any topicals? Maybe using some Retin-A Micro to help with the stubborn areas you mentioned. I also have really good luck with Benzamycin on particular break outs. I also love Green Cream it's .06% Retinal and works great especially with discolorations and over all clarity of the skin. HTH