tl;dr: The Bussard collectors are there for emergency situations, and it's complicated.
Welcome to the magical and slightly convoluted world of starship propulsion technology!
Regular use of the warp nacelles
Spaceships of the United Federation of Planets are equipped with warp drive systems which uses a combination of two kinds of fuel:
Both kinds of fuel are stocked in advance, and are not collected from the intersteller medium.
The fuel is used by first converting the Deuterium into some combination of gasses (?) ; and that gets intermixed with the Anti-Hydrogen in the ship's warp reactor core (which is not in the nacelles). This produces highly-energetic "drive plasma", which is transmitted via EPS conduits to the nacelles, where it is intermittently injected towards the warp coils. Energized by the plasma, the warp coils generate the warp field that makes the ship move faster than light.
annihilating EPS -=|magic|=-
Deuterium + Anti-Hydrogen -> Plasma -> Plasma in drive coil -> Warp field
You will note that no fuel gets to the nacelles at all in this process. Thus, the Bussard collectors have no use for anything when the ship is at warp, and it shouldn't matter where they're placed, if at all. But - we're not done yet!
There's also the way ships are driven when they're not at warp, or not warp capable - the Impulse Drive (a.k.a. Impulse Engine). It's actually quite similar to how warp driving works:
fusion EPS -=|magic|=- +
reaction conduction plasma venting
Deuterium -> Weak plasma -> Plasma in drive coil -> Sub-warp-1 field
Why weak plasma? Since we get it from nuclear fusion, as opposed to a matter-antimatter reaction - a fusion reactor vs. the warp core reactor. This part is non-fictional physics: It's well known that the former is much less energetic than the latter, since in the fusion reaction you shave off a lot less of the mass involved.
As for drive coil used - that can be either a coil dedicated to impulse driving, or, in fact, a warp coil: Those can be used also for the weaker impulse-driving (see also the description of impulse drives at Ex Astris Scientia). And it is at this point in the discussion that Bussard collectors may finally come in.
Emergency + Bussard collector + coil = propulsion
Suppose your ship is in trouble, with one of the following happening:
- You're out of warp drive fuel
- Your warp core is damaged
- You've jettisoned your warp core
- Your EPS grid is damaged
Now, according to the Federation Starship Datalink website, and specifically this page about warp engines:
When plasma is unable to reach the warp nacelles, the Bussard ramscoop assembly at the front of each nacelle is able to draw in low-grade galactic matter and use this as an energy source instead.
Well, we already know what it means to "use as energy source": Dump it into a reactor; and since we only scoop regular matter, not anti-matter, from the interstellar medium - it has to be a fusion reactor. This only gets you weak plasma, not the warp plasma you usually get from the warp core; but no matter: we noted the warp coils in the nacelles are usable also with the weaker plasma. So, you can cruise on home despite your emergency, albeit at a rather slow speed.
That is also the likely explanation of why the collector is part of the nacelle (although I am speculating here): The emergency situation making you use the collector in the first place is not being able to get plasma to the nacelle. Now, some of the reasons for that would still let you put the collector elsewhere and send the weak plasma over the EPS grid. But the more robust thing to do is have a collector right next to the warp coils: You're protected against EPS grid or other structural failures, you don't have to worry about saucer separation, and finally - each nacelle is now a self-contained impulse drive unit.
Note: If we look at the diagram for a Sovereign-class nacelle, we'll notice an element named a "fractionator". They is likely an Isotope fractionator, for choosing which collected isotopes actually get used in the fusion reaction. It's likely not for keeping just the Deuterium, though, since there's only 10^-5 as much Deuterium as there is Hydrogen, and there's not much Hydrogen... One would guess that Bussard-collected fuel is not as convenient as Deuterium.