Gary Smith said the timing of the opening goal just after the interval was crucial after Stevenage's 2-0 defeat at Charlton.
Michael Morrison broke the deadlock four minutes after the break with a stunning shot from just outside of the box and Charlton's top scorer Bradley Wright-Phillips, without a goal since November 19, made the game safe in the 64th minute to ensure the Addicks gained revenge for a 1-0 defeat at Stevenage earlier in the campaign.
Smith said: "In the first period I thought we competed well, not enough of a goal threat, but in saying that we still had a fabulous chance just before the break when Luke Freeman might have done a tad better on the cross that was worked in towards the back post.
"The goal just after the break really separates the teams and gives Charlton a huge lift. It's always nice to score coming out of the half-time break quickly. It gave them a little bit more of a spring in their side and of course the second goal makes life a little bit difficult for us.
"All in all I thought yet again the determination and the spirit of the group was never at fault.
"There were one or two really important moments in and around Charlton's final third that we just looked lacking in a bit of creativity. One or two of the choices were a bit array, but we've had a tough run of games."