McFadden netted his first Scottish Premiership goal of the season during a fine individual display, while Keith Lasley, Zaine Francis-Angol, John Sutton and Lionel Ainsworth were also on target against the outgunned hosts.
McCall, who played McFadden just off centre-forward Henri Anier, said: "We know Faddy would like to play in that position but when you have Sutton and Anier, who have formed such a good partnership...
"But today we felt we needed pace in wide areas to stay with their full-backs and it's such a big park, we don't want to play two up.
"Faddy playing in that area is probably his best position. How many times we play that way is there to be seen.
"But I was delighted for him because he has worked hard. He made a goal for Lasley and you could see his old confidence come back. He hits the bar and could have had another one.
"It was an outstanding performance, one we know he is capable of. Hopefully it kick-starts him into action, as long as we can get him a lot of time on the grass."
McCall was pleased with his side's ruthless response after Steven Lawless had fired Partick ahead.
"I thought we were a bit fortunate to go in at half-time 3-1," he said. "Thistle started the game really well, wee Lawless got a terrific goal for them and I thought he was coming back to haunt us.
"But we got some really good footballing goals. It's a big park, they like to play, so I thought it would be an open game, which it was. And we were just clinical.
"The second half was difficult for Thistle, they had to come at us and we defended strongly and picked them off on the break. We could have had more after that but they certainly played their part in the first half."
Thistle boss Alan Archibald gave a scathing assessment of his side's defensive display.
"I thought it was embarrassing," he said. "The second-half performance was unacceptable. We had a go in the second half and left ourselves wide open.
"We started the game very well, made a number of chances and got the goal, but I thought Motherwell were more professional and precise, and individual errors cost us.
"It's probably naivety, after we scored the one we kept on trying to get more. We probably should have got another one but Motherwell went up the park and capitalised on our mistakes.
"They didn't have to work hard for their goals whereas we had to cut them open to get our chances."