You ask about redirecting STDOUT and STDERR for system calls given as lists. A good way to do this is with the module IPC::Run.
use IPC::Run qw( run ) ;
run \@cmd, \$in, \$out, \$err;
One idea you might be able to use for parameterizing your error messages for various commands would be to pass in a hash reference containing explanatory messages indexed by return codes. Also see perlvar for how you can use the variable $! to obtain error message strings after a failed system call.
Finally, the reason spelled-out file handles are considered "bad style" compared to IO::File is that they create global names, which might conflict with other modules. IO::File uses unique private symbols instead. | 