The movies after TMP are an unusual situation. There's no specific "mission" in III or IV as far as Starfleet is concerned, so Chekov's role in each is obviously hinging more on Kirk's faith in his abilities, just as with the rest of the crew.
In V, Chekov, carrying the rank of Commander (and thus whose superiors are limited to Kirk, Spock, and possibly Scotty) is seen taking command (even when Scotty is still aboard) when not assuming the navigator position.
Being that Chekov was part of starship security/tactical/weapons control/whatever during the series and in TMP as well as part of TWOK, it makes sense the novels would include this as part of his duties. But Chekov was also a backup science officer and (I'd always assumed) Terrell's XO on Reliant as well, so he really fits the description of "jack of all trades."
At least, this is how I've always interpreted it.
In VI he's back to his position as navigator, likely because its the last tour of duty before they all retire and is Spock's de facto XO (again, superseding Scott not by rank but by position, aiding Spock and Valeris in their investigation.