One plays the tanpura in the background to help
fix the pitch of your playing. Since you have a flute
that is set to the A-scale, set the tanpura to the pitch
A. Set the first string to Pa.
The reason for choosing Sa and Pa to be played on the tanpura
is that these notes are "fixed" in all ragas, so having
a constant drone playing these notes in the background gives
you a base which you can rely on to fix your pitch while
playing the flute.
I might add that @Rusi is not incorrect in saying that what
note is played on the first string of the tanpura depends
on the raga being played. However, it is enough to keep
this as a general rule as a beginner that the tanpura
is set to the pitch you are playing and that the first string
is set to Pa.
Do not change the tuning of the tanpura as per the notes you
are playing: that would defeat the purpose of having the tanpura.
The tanpura is not an accompaniment to your music, in the sense
that it does not follow the notes you play. It stays constant
in the background to provide a base for your playing. Use the
Sa and Pa played on the tanpura to understand the positions of
the remaining notes (Re, Ga, Ma, Dha, Ni) as well, in relation
to Sa and Pa.
This is the primary function of the tanpura. However, I do not
deny that playing the tanpura also lends a pleasant ambience.