from what i believe, i think you're getting a couple of things mixed up...

there are 'dopplegangers' and there are 'inhabiting spirits'
but to explain it, you gotta get into a long story of TP mythology.
i'll try to explain from what i personally believe, and i'll try to make as much sense as i can...

Hawk made reference to his heritage believing in a place known as the white lodge, a place analagous to heaven, and to gain entrance into this wonderful place, you must have perfect courage, because when you enter you are faced with your doppleganger, an exact but opposite version of yourself.
if you face your doppleganger with imperfect courage, your soul would be annihilated.

Windom Earle makes reference to a vile, evil place of horrible demons and anger, but also filled with unequalled power, known as the black lodge, a place analogous to hell

in the final ep,
the LMFAP warns coop, "when you see me again, it won't be me" and we see what we believe to be another LMFAP and another Laura, but both with weird eyes and maniacal behaviour.
at the end, we see an 'evil coop' smash his head in the mirror asking,"how's annie?" just before we see an image of BOB in the mirror (showing that the two are going to be 'working' together, not that BOB posesses coop)

ok, so what the hell does it all mean?
so there's a white lodge and a black lodge, connected by a red 'waiting' room (in coop's case anyway, but that'a another story).
one good and one evil, each having it's own minions and servants.
in preparation for some battle at armageddon or whatever cataclysm your religion dictates, they each want to 'recruit' as many minions as they can.
the white lodge offering peace and happiness,
the black offering power... raw unadulterated power.

however, not many of our world even know such places exist...
those who don't know at all we'll call the 'innocents'
those who do know we'll call the 'gifted'

the gifted are inexorably drawn to one of the two opposing sides,
the white lodge, making them primarily good, we'll call them the 'blessed'
or the black lodge, making them evil SOB's, we'll call them the 'damned'
(let's say blessed and damned because we're biased in the naive belief that most would strive to be 'good' people)

examples so far...
innocents:almost everybody
gifted:Laura Palmer (she had a good idea of what was going on but didn't really try to        do anything about it)
blessed:special agent dale cooper (of course), and maj Briggs
damned:the irreplacable Windom Earle

got it?
ok...

now each of the lodges have a number of their own spirits and minions, servants or troops or whatever... those that do the will of whatever powers that be in the lodges

these normally take the form of owls (theoretically any other animal as well), they observe what goes on in our world and occasionally may perform errands

but there are others as well, like the inhabiting spirits... those who can posess ordinary people in our world (but with some limitations)

i'll tell the story of MIKE and BOB in another post... but for now it'll just be the basics...

BOB and MIKE used to kill for the BL, but MIKE reformed and cut off the arm that he killed with. now MIKE's only mission is to kill BOB.
MIKE inhabits Philip Gerard (the one-armed man), and for a time BOB inhabited Leland Palmer
from time to time, the inhabiting spirit would be able to 'take control' of the person they are inhabiting, and they are then able to do whatever they wanted, and the person they are posessing would have no knowledge of what they did while they were under the influence of the IS.

MIKE continued to 'hunt' BOB, until Phil Gerard started injecting himself with haloperidol,an anti-psychotic drug used primarily for schizophrenia, which would help to supress MIKE's taking control.this allowed BOB to continue what he wanted to do, feed off the intense emotions of his victims, then taking their souls

the giant is another inhabiting spirit, he inhabits the waiter at the Great Northern (Sr Droolcup), who primarily seems to act as a 'guide' for the blessed

the LMFAP seems not to be an inhabiting spirit, but a minion of the white lodge who is a 'welcome party' to the red room

minions of the BL, or dugpas, wish to gain more power by taking the souls of the innocents, but the WL appears to not be totally powerless in this matter...
in some cases, they can protect the souls of some of the would-be victims by encasing them in wood, which apparently keeps the minions of the BL away from them
i think this is because wood is a strong element associated with the white lodge, where fire is associated with the BL
there are more symbols and such, but i can get into that later

this 'protection' was the case of the Log Lady's husband, and in the case of Josie Packard (BOB didn't kill her, he was just drawn there by the intense emotion of the situation and to gloat to coop)

now the doppleganager situation,
the lodges exist in both a physical and a mental state, on a different plane of existance than our own
but there are places in our world where there is a connection to the physical aspects of this other world