Great to hear this is being used in schools!
From your description I assume you're using TEXT to display the question rather than PRINT. INPUT displays the input in the same way as PRINT, by writing to the "output stream" as you might call it. That was a bit garbled, here see for yourself:
cls 128
ink 65535,1
set cursor 200,50
print "Hello"
print "World!"
input a$
set cursor 200,70
input a$
As you can see, set cursor only applies to the next output. Since I flooded the background you can also see that input doesn't really "delete" characters, it just overwrites them with the second colour attributed to INK. (This is also the colour that CLS will use if you don't specify a value.) SET CURSOR only effects the output stream.
Go with Zero's solution for now, INPUT is ugly and there are ways to display input in a nicer fashion using the keyboard entry buffer, but that takes a bit more work. Maybe that could be your next challenge!
Here are some commands you might like to read up on:
ENTRY$()
CLEAR ENTRY BUFFER
ASC()
CHR$()
MID$()
LEFT$()
RIGHT$()
^ That's what she said.
