Which of these is cheating?

Lately I have modified my flying methods in the sim in ways that seem
to produce better results, but I don't know if I'm learning to do
things correctly or simply acquiring bad habits. I want to make sure
that I don't "cheat" too much when flying.

For example, lately I've had a tendency to adjust climb or descent
rates (and altitude to a lesser extent) by making thrust adjustments,
rather than changes in pitch. I seem to recall someone telling me
that this was legitimate, but now I can't find the reference.

Anyway, on approach in particular, I've been using the throttle to
adjust descent rate rather than pitch, the reasoning being that
changing pitch just shifts inertia to a different place, from which it
will return at some point, nullifying the effect of the change in
pitch. For example, if I just point the nose down to descend towards
the airport, airspeed increases, and as soon as I ease off the yoke
I'm climbing again. If I try to climb with pitch, my airspeed drops,
and so I end up descending again shortly thereafter.

So I figure that if I reduce thrust, I reduce lift and inertia, so any
loss of altitude will be durable (unless I increase thrust again). If
I increase thrust, I add lift and inertia, and I climb. Is this the
way I'm supposed to be doing it?

In a related vein, I was wondering how legitimate it is to lower flaps
just for the sake of increasing drag, at low speeds? Lately I've had
a tendency to lower flaps not so much to increase lift on approach,
but just to slow the aircraft down and absorb inertia (which in turn
increases my descent rate). I use flaps much later in the small Baron
than I would in a 737. Once I lower them, I maintain altitude with
increased throttle. I get the feeling that I'm in a more stable
configuration with full flaps and a higher throttle setting than I
would be with no flaps at a lower setting, although I'm not sure what
is giving me this impression.

I have tried to roll to fix runway alignment rather than just using
rudder. However, I still use the rudder when very close to the
runway. For example, if I'm slightly misaligned at 50-100 feet, I
will use some rudder and hold it in order to stay aligned as I touch
down. At higher altitudes, I try to roll into position instead.

I sometimes increase throttle in the last 100 feet or so above the
runway to make sure I don't get too close to a stall. I don't always
land with throttles idle, unless I'm only a few feet above touchdown
and there is no wind (which seems to be rare, if I'm using real-world
weather).

I have consistent problems getting properly aligned for landings
(although in some cases I'm simply too close when I turn to final, I
think). I also tend to be much too high when I come in. I have a lot
of trouble with patterns, turning to final, when I often discover that
I'm parallel to the runway but a quarter-mile off to the left or
right.

For some reason, it always seems that I start to drift out of
alignment in the last 100 feet above the runway. I don't know if this
is from surface-level winds or what. And, unfortunately, controllers
in the sim don't announce surface winds on take-off, even though I've
heard them do this in real life ("wind two seven zero at niner"), so I
have a hard time knowing the wind unless I check the sim or happen to
spy a windsock somewhere.

So, what mistakes am I making?

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