I'm pretty sure that you'll get erroneous results if you try to profile both simultaneously.
But there's a simple solution to that: set the environment variable NYTPROF to addpid=1, then the profile for each process is written to a different file.
Then one can either analyze each file separately with nytprofhtml -f nytprof.out.$PID, or run nytprofmerge -o nytprof.merged nytprof.out.*; nytprofhtml -f nytprof.merged to merge them all into one report.
And to make sure that all perl processes are profiled, one can set the PERL5OPT environment variable to -d:NYTPProf.