Hi there Pumpkins!
You can either fill up the online application form , then print it
OR
just print the form first then fill it up (hand written).
I think the paper VAF and online application are merely options for us
applicants (for our own convenience). I remember sending an email to UKVACS about it and they said whichever way you submit your application (online or hand written) there's going to be
no difference in processing time.
For me and my son, I chose to print it out and fill it up hand written, it will be easier for me to check (and recheck) my answers.