I agree with Shailendra and Anand.
Your business has set parameters around this process that you cannot resolve on your own via QM. (i.e. the no change to external software requirement). Anytime you integrate systems it takes two to tango usually.
To control your process as you want will take significant development and testing and careful design. Not someting we can give you a great amount of help with since we really don't know the finer details of your business or your thrid party software and what it does or is used for.
Craig