It's perfectly reasonable to run multiple scripts against a tune to get the final solution. The most obvious application of this is what I described in the "Building DSP5 Segments" section, but don't be limited by that. You can write scripts for anything. If enabling or disabling some feature, DPF delete for example, requires changing more than one parameter, creating a script for that one change will insure you never make a mistake when applying that change.
If you're really clear on what you're doing and understand the structure of script files you can do all the changes, make a script and then use an editor to carefully cut it up into little pieces. If you're more of a mortal than a superman, you're probably better off taking a stock tune, making a copy, making one class of change at a time and then building a script for each set of changes.
If you find scripts useful, you will probably end up with a lot of scripts. Working with them will get easier if you build a directory structure under the scripts folder. For a diesel tuner it might look like this:
Scripts
LB7
LLY
LBZ
LMM
A40
AL5
And then if it seems important, you might add more folders below those. When you're saving a script there will be an Add New Folder button somewhere up near the top of the save file dialog box, or you can usually right click in the file list box and choose New and then Folder in the menu that appears.