Here's my take on what the autofire/multifire rules mean. It's a bit of a
mish-mash in the rules.

Weapons are classed as Standard, Multifire, or Autofire. Additionally,
some "Standard" weapons (at the DM's discretion) are not capable of fast
operation at all. In the current game all weapons are either Standard
(mostly rifles) or Multishot (mostly revolvers), which is just as well
because Autofire is a mess.

Normally you use one bullet per attack roll. You can never, ever, get more
attack rolls than you had bullets to fire.

All your attacks are always resolved at once, in the normal initiative
sequence.

If penalties mean that a natural 20 isn't enough to hit, you still hit,
but you can't do a critical hit.

Ordinarily, you get one attack a round. If your Base Attack Bonus is +5 or
better, you get an extra attack at -5 to your BAB; +10 or better, another
extra attack at -10, and so forth. This only matters at high character
levels, but if you get this bonus attack, you get it independently of any
others, without any penalty to your first attack, and on any weapon where
it isn't inherently absurd (eg, on a muzzle-loading cannon that could only
be loaded every few rounds). Additionally, your extra attacks can be
directed at any target you please.

Every other multi-shot option requires that you be proficient with your
weapon, that it be inherently capable of fast operation - modern firearms,
or bows (but not crossbows) in the hands of proficient users, and that you
direct all shots at the same target. ("I would like those chaps over there
to keep their heads down" is "a target" - something's a single target if I
say it is.)

If you have the Rapid Shot feat, you can take an extra attack with any
weapon, suffering a -2 to all attacks that round. This is independent of
all subsequent options. You decide to use Rapid Shot when making your
first attack. You can choose to hold back your second attack (eg, if the
target was eliminated.)

With a Standard weapon, you can make an extra attack, suffering a -6 to
all attacks that round; -4 if you have the Multishot feat. You decide to
do this when making your first attack. You can choose to hold back your
extra attack.

With a Multifire weapon, you have the same option, but the penalty is only
-4; -2 with Multishot.

So when you first make an attack, you choose to fire either one or two
shots - or three with Rapid Shot. You calculate the penalty to hit, roll
your first attack, and choose whether or not you want to actually take the
second and third shots. After those, you might have extra attacks at -5
or even -10 because of your giant base attack bonus; you also choose
whether or not you want to take those.

Notes for autofire (here there be dragons, this isn't really written for
players):

With an Autofire weapon, you can make two extra attacks, suffering a -6 to
all attacks that round, -4 with Multishot. You can't hold back; once you
pick Autofire, you're making three attack rolls. Or four with Rapid Shot,
but you can hold back on the 4th.

OR
You can make one attack (or two with Rapid Shot) exactly as if the weapon
was Standard. If the weapon has no semi-automatic firing mode, the very
first attack uses three bullets (up to the number available), even if that
denies you a later attack.

OR
If the weapon has a semi-automatic firing mode, you may fire two shots (or
three with Rapid Shot) exactly as if the weapon was Multishot. This uses
the number of bullets actually fired.

ALSO
If you picked the first Autofire option, you can choose to keep the
trigger down, spraying bullets indiscriminately. You fire three more
bullets, making _one_ roll to hit with an additional -4 penalty (not
cumulative with Rapid Shot). And... you can keep doing this as long as
there are bullets in the gun (even if your last segment of fire uses
fewer than three). At the DM's discretion, this may be effective in a
target-rich environment. Extra attacks from high BAB are interleaved -
spray at -4, -5, -8, -10, -12...