Sulley Muntari and Keisuke Honda struck the goals for the Rossoneri.
"We have these two systems and Bonaventura allows me to change even during the game. He did well in that new role, although obviously better in the position he's more accustomed to," Inzaghi told Sky Sport Italia.
"We almost conceded the equaliser on the counter from a corner, which would've been terrible. We kept a clean sheet tonight, even though we allowed too many chances. Perhaps we are too generous in pouring forward.
"At least the fans are entertained and we are the top scorers in the League this season."
Menez has made it clear he prefers to play a more central role behind the striker, so not in the 4-3-3.
"He probably does feel better there, but I cannot build my team around one player and have to work on everyone.
"I thought that by changing system and opening up the field we could create more opportunities. It was a good response from the squad and I expected that, as I saw them work hard throughout the week."
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