When setting up the first (open) section, it asks the question "Is
this a flighted event (A different section exists with an upper
masterpoint restriction concurrent with this game)?"
It seems clear that you answer yes to this question.
Then you are asked "Number of tables in the lower masterpoint
restricted section(s)". In this case you would enter "5" as the
number of tables in the limited section. (Although I don't see how
you would change that later if you had a sixth table show up at the
last minute.)
But I think the key question is when you start to set up the second
(limited) section and the first question to answer is whether this is
a separate event. Common sense says you should choose that is the
same event (one event, two sections), but then you are never prompted
to put a masterpoint restriction or stratification for the limited
section. So it may require saying the limited section is a separate
event, although that seems counterintuitive to me.