The Hornets have made wholesale changes to the squad that won promotion from the Championship last season, with seven new recruits featuring in the goalless draw against Southampton on Sunday.
Three of the club's new signings, however, failed even to make the bench at Vicarage Road, including Matej Vydra, who saw his loan deal from Udinese made permanent in July but is yet to play a minute under Flores this term.
Flores does not have final say on new players as he forms only part of Watford's transfer committee, and the Spaniard admits it has been a challenge to keep everyone happy so far.
"It is difficult because I want the players to feel happy," Flores said.
"We have a lot of players who are not on the list and there are a lot of players who want the possibility to play.
"We are a new team and we are creating a new base
Everything is new
We have how many new players? Too many.
"It is important not to create bad feelings with the new players."
Watford currently have 21 foreigners on their books but will only be able to name 17 in the final 25-man squad submitted to the Barclays Premier League.
It means the club are likely to offload a number of fringe players before the end of the window but Flores believes there are likely to be more incomings too.
"Will there be more signings? Probably," Flores said.
"Because we have been working this way for the last two months to complete the final squad."
Southampton are hoping to avoid drastic changes to their own squad, with Sadio Mane and Victor Wanyama reportedly attracting interest from Manchester United and Tottenham respectively.
Ronald Koeman reiterated his stance on Sunday that neither player will be sold ahead of the transfer deadline, while the Dutchman is keen to add another defender to his ranks.
The clean sheet against Watford came as a welcome boost for Saints, who deployed three centre-halves after conceding five goals in their opening two league matches.
"It was to give us a little bit more sureness defensively," Koeman said.
"When you change the system it's always about the players you have.
"Last season we played four or five times out of this system and after the five goals we had conceded it was a good time to change."
Source : PA
Source: PA