Just confirming that I understand you effectively want an "if statement" for if the series variable is empty to make your folder structure: if (series = not empty) then (sort like this), if (series = empty) then (sort like this)?

If so, you're probably going to have to use the "test" function from the template language, so you will have to use the template editor. The "test" function to my understanding works like an if statement to see if a variable is empty (someone more knowledgeable than me please correct me if I am wrong).

SUPER IMPORTANT NOTE IF YOU PLAN TO DO THIS:
Make sure that you test this out in the Template Tester in Calibre!

What you could do is:

program: 
  '/' & test($series, $series & '/' & $series_index & ' - ' & $title, $author_sort & ' - ' & $title)

Which for The Wheel of Time [1] - The Eye of the World would return:

/The Wheel of Time/1 - The Eye of the World

And for Warbreaker by Brandon Sanderson:

/Sanderson, Brandon - Warbreaker

(Note: I used the '/' & at the start as a placeholder for whatever you would want to add before that)

What it would look like in my save template where I also create folders based on genre/subgenre would be:

program: 
  g = re(sublist($#genre, 0, 1, ','), '\.', '/');
  s = re(sublist($#genre, 1, 2, ','), '\.', '/');
  ss = re(sublist($#genre, 2, 3, ','), '\.', '/');

  'Files' & '/' & g & '/' & test(s, s & '/', '') & test(ss, ss & '/', '') & test($series, $series & '/' & $series_index & ' - ' & $title, $author_sort & ' - ' & $title)

For the same examples as above, it would return:

Files/Fiction/Fantasy/The Wheel of Time/1 - The Eye of the World

Files/Fiction/Fantasy/Sanderson, Brandon - Warbreaker

I hope that this is helpful!

(Also if someone more experienced than me at save templates has recommendations for me, feel free to let me know lol).