A piping technique can be used to send several commands to external tool.
Let's take the standard "cmd" as an example. Let's assume you have a text file with a list of commands you want cmd to execute. Let's name this file "c.txt" and have the following lines in it:
ECHO Let's execute DIR command... DIR ECHO Done! ECHO Now let's see some help for CD command... CD /? ECHO Done!
Note: Don't forget to press Enter to have end-of-line (CR/LF) after the very last line! As far as I understand, the last command ("ECHO Done!" in our case) may be incorrectly understood if there's no new line after it.
Now execute the following from NppExec's Console:
cmd /C type c.txt | cmd
I believe the same technique should work with external tool as well - e.g.:
cmd /C type c.txt | external_tool
unless the external tool itself does not accept piping. But generally this approach should work.
See also: Using cmd.exe [4.4].