For your first question, if you have time, would you be able to share your data and workflow steps with me as is so I can try to track down that Error 999999? We are always trying to flush those out and get rid of them, so if you have a consistently reproducible instance of it, I'd like to log a bug for us to fix it. I can't tell from your description so far whether this happened when creating the network dataset, solving, adding locations, etc.
But, ultimately you need a way to get up and running with your Service Area analysis. If you haven't already, please walk through the tutorial for creating network datasets. You might also find useful this set of downloadable Tasks for creating a local government network dataset from street centerlines.
If those resources don't fix the problem, please post more detail about exactly where the problem is occurring and share your data if you can. (You can message me privately if you don't want to share your data publicly.)
For your second question, you can automate Service Area calculations using Model Builder or Python. Here are some resources that will help:
