I have heard that practically such advice is decided by the Prime Minister, though I am interested in the formal process behind this.
Such advice is decided by the Government. The idea that the Council itself presents advice is one of those quaint little fictions that underpins the UK's constitution. There's no vote of the Council or anything like that; the full Council is 701 strong and sits on very few (purely ceremonial) occasions. The Government's internal process for deciding policy varies from Prime Minister to Prime Minister. Some favour a more presidential style, others a more collaborative effort in Cabinet.
Once Government has decided the advice it is conveyed to the monarch by at least 3 (the number required for a meeting of the Privy Council to be quorate) Privy Councillors. Their reporting the advice to the monarch is the meeting of the Privy Council from which "Orders in Council" derive. For example, here's the Order in Council ordering the Prorogation that was intended to take place in early September. The actual order is on Page 4, and reads:
It
is
this
day
ordered
by
Her
Majesty
in
Council
that
the
Parliament
be
prorogued
on
a
day
no
earlier
than
Monday
the
9th
day
of
September
and
no
later
than
Thursday
the
12th
day
of
September
2019
to
Monday
the
14th
day
of
October
2019,
to
be
then
holden
for
the
despatch
of
divers
urgent
and
important
affairs,
and
that
the
Right
Honourable
the
Lord
High
Chancellor
of
Great
Britain
do
cause
a
Commission
to
be
prepared and issued in the usual manner for proroguing the Parliament accordingly
n.b. "divers" is an older spelling of "diverse".
So; government decides and sends not less than 3 Ministers, all of whom are Privy Councillors, to the monarch. They report the advice to the monarch, and that meeting is the Council from which Orders in Council are issued.
The Privy Council's website does a decent job of explaining this: https://privycouncil.independent.gov.uk/orders/
One might wonder what would happen if some Privy Councillors who are not ministers went to the monarch and issued advice. For example, what if the Opposition (some of whom are Privy Councillors) decided to advise her to issue an Order in Council. The answer is, pretty obviously, the Palace would call up HMG who'd send some heavies to turf them out. How this would be justified legalistically is a question for law.se, but the Political response is that constitutional convention is that only those Privy Councillors whom are also Government ministers give advice.