Your topic is a bit confusing. Why do you find it necessary to edit the JCL everytime and then submit it? Can't you use some other method of providing the varaiable values? Can't it get the changes from a dataset of some sort? I suspect that the question you're not really asking is, can you make changes to an application running on TSO that affect a running job? The answer is no. Batch and TSO are two seperate address spaces and have no relationship with each other.
Anyway, you haven't told us what your real goal is. Can you have a program that runs in TSO and calls a panel where you can enter your changes? Sure. What do you want it to do then? You could have your program edit the JCL, apply your changes, and then submit it. Or you could use ISPF File Tailoring Services to build JCL with the changes added dynamically.