Ok, I figured out how to do this. Basically instead of entering the inputs as individual commands the inputs are entered into a text file.
commandfile = fopen('commandfile.txt','w');
fprintf(commandfile,'Enter inputs to read in executable here');
fclose(commandfile);
system('executable.exe < commandfile.txt'); % I used the system command here, rather than evaling '!'. I believe they both would work, but I decided to stick with system from another user.
By using the actually command prompt command of 'executable.exe < commandfile.txt' command prompt knows to run the executable and read the command input text at the same time, allowing for commands to be entered into the executable.
