In the PS2 version, R1 locks your gun onto the target, so whatever keyboard
button that's assigned to for the PC ought to do the trick.  When you hold
up a store, you lock your gun on the target, and money should start
appearing on the counter- the longer you hold your gun on the target, the
more money will appear, but the higher your wanted level will grow also.

You don't actually find money, but your net worth should go up while you
have a gun pointed at the store guy.

If you have one of the sniper guns, the right mouse button will do that.

Using any weapon, pistol, shotgun etc aim using the mouse and keep the
target over the storekeepers torso.  Your gun will never raise unless
you are shooting but somehow the storekeeper knows you are aiming at
him and after a few seconds he will kind of look up and money will
begin to spawn onto the counter.  The longer you hold the gun on him
the more money will spawn and the more your wanted level will raise.
If you just want to rob the store for 100% then just wait for one pack
of money.  You must run over the money and "grab" it for the the store
to be robbed.  If you just scare the clerk into putting the money on
the counter and you leave it there then the store is not robber and
will not count to 100%.  There is no way that I know of to know if a
specific store has been robber or not. You just have to keep track of
the stores you have robbed.  Go to each store until your stats read
that you got them all.

Good luck!

If your wanted level went up, you probably did it right.  If you're standing
right next to the counter where the money appears, you'll automatically pick
up the cash before you even see it, so that's probably what happened.