Latics reached the showpiece for the first time in the club's history with a 2-0 victory over Millwall, 53 years after Whelan broke his leg playing for Blackburn in the 1960 final.
"Yes, we will get the chairman leading the team out," Martinez confirmed. "It will bring full circle his time with the FA Cup."
Asked what reaching the final means, he said: "It means a lot as you can imagine. Not just the first time we're playing in a semi-final but the opportunity to reach the final, it's a big, big achievement for the players and they deserved it.
"So do the fans. A lot of people judge us on the numbers but it's about the quality of the numbers."
He admitted Millwall made them work hard for it: "We did expect that. Huge credit to Millwall who competed until the last second and there were plenty of difficult situations as they can be quite powerful.
"To handle being the favourites in a semi-final can be tough but I thought we did that magnificently, from the young players to the experienced players there was a real togetherness."
Shaun Maloney and Callum McManaman scored the goals, and Martinez had praise for the latter, who will make the headlines for the right reasons after his nasty tackle on Newcastle's Massadio Haidara on his Premier League debut last month.
"It's great to see that it's now all about his talent," Martinez said. "He's an attacker, not a defender, and who can see that in how he takes the goal. He seems like he's been playing at Wembley many, many times.
"The whole situation has been very, very unfair on him, he was in the wrong place at the wrong time, but today we saw the real Callum McManaman."