While Carroll is set to take a breather and play no play no part in Tuesday's Carabao Cup third round clash against Championship strugglers Bolton, it remains an issue which is troubling Bilic.
Carroll has featured only twice in the Premier League this season after four months out with a hip injury.
Poacher Hernandez, a £16million summer signing from Bayer Leverkusen, has been forced into a less-than-ideal wide position at times as West Ham seek stability to stop their run of defeats from the start of the season by playing a three-man defence.
"I am thinking about them the most but it is hard to have them both in their natural positions", said Bilic.
"It is hard to do that and then have three at the back, then with [Michail] Antonio and [Marko] Arnautovic, it is nearly impossible". Chicharito is at the moment playing in a position that is not his ideal position.
Carroll, who has been plagued by injuries throughout the years, has made only two appearances this season as he continues to recover.
While the former Croatia manager is hopeful Carroll stays fit following his latest return from injury.
"Of course we have to manage him", he said.
"We are managing him, to be fair, a little bit differently this season". We didn't buy him just because of that but also one of the reasons why he was great for us was because they are two players that can play with each other.
How numerous Carabao Cup team will be present remains to be seen, however, after Bilic made 10 changes including the return of captain Mark Noble from a knee injury.
"It's a big game for us and that is all we think about", he said.
"We are very ambitious within the club and if you have a look at the round we played a few weeks ago, most of the clubs put strong teams out". 'He's just done a scan and it's not ideal but I expected worse based on how he got injured'.