Should I make a new level of subroutines to have less repeating code? (In other words, my subroutines would have subroutines.) It seems that might be more confusing to decipher later.

If you name your (sub)subroutines well, to reflect what they do in the context of the callers, it can often greatly clarify things

Which way would be more efficient running the program?

You do pay a performance penalty for calling a subroutine. In any language, but usually more so in interpreted languages.

Or would it matter at all?

Whether the reduction in maintenance -- of not having to change (and remember to change) all the copies of similar code -- and the clarity and greater readability that can come from having smaller subs; thus less code to deal with at any given time -- is worth the performance cost -- is very much down to how critical performance is to your program.

If your program runs for a few minutes a couple of extra seconds don't matter much. If your program runs for hours and the extra subroutines add another hour or two; you might reconsider the balance.

If your program is IO-bound: eg waits for the user to fill in a web form; a few seconds might not matter too much; but a couple of minutes might loose you business.

Only you can know your application well enough to know the right answer to that question.