Many ways to skin this cat. Need more info though.
You can only have one piece of stock, unless you make a "multiple fixture" program.
Are you using solid models and feature recognition? (I do not recommend that approach)
If you are willing to email your part file, I could set one up for you real quick. Then you could take a look at how I did it and modify as you see fit.
I use this technique all the time! (many parts from one piece of stock)
I am assuming part 2 is the second operation of part 1?
In this case, you can actually save your simulation results of part 1 as an .STL file, and use that solid as your stock for part 2.
There will be lots of transform action to get everything where it needs to be. But, it works slick.