What you call atomic, most people call "error handling". die/eval is the standard Perl way of doing throwing and catching errors, similar to try/catch in Java. So, yes, die is what you want to do.

One more thing - you might want to look at named pipes instead of system. That way, you can parse the input of the command, if you want.

One more thing - you might want to take a look at the $? variable, which is set by the system() function. Read up on system.

One more thing - if the scripts are their own entities, it is a good thing. However, I would recommend looking at refactoring the functionality into various modules and packages, to benefit from code re-use.

One more thing - it looks like you're doing some sort of batch processing. There are very good applications that have already solved this problem, plus provide features you'll never think of. You might want to google for "batch process open source" and see what comes out. If your employer has the capital, I'd recommend either Oracle Scheduler or Control-M, for proprietary products. Stay away from Tivoli and SQL Scheduler.