Arsenal take on Liverpool at the Emirates on January 6 in arguably the blockbuster fixture of the third round.
Sunderland host bitter rivals Newcastle in the Tyne-Wear derby, and Manchester City welcome Huddersfield to the Etihad.
Making his debut on talkSPORT Breakfast alongside co-host Ally McCoist, Stelling believes it is time the draw is seeded so lower league sides can receive a bigger payday.
"I'm not interested in Arsenal against Liverpool in the FA Cup, I see it in the Premier League, not interested at all," he told talkSPORT.
"What worries me is some of the smaller teams who get through to this stage. You look at Eastleigh and Maidstone, they played five games to get to this stage and they are looking for a bumper payday.
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"And what happens? They get a rotten draw. No chance of TV coverage by the way, no chance of a big payday.
"What they need to do is seed the third round draw of the FA Cup. For goodness sake, it is not too difficult."
Stelling added: "We have got 20 teams who qualify. They've come through round one and round two and all the qualifying rounds before that.
"You pick them out of the bag, home or away, and then you put the rest of the teams from the Premier League and Championship, all 44 of them, and you pick out 20 of those teams and they will play the lower league sides.
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"So every lower league team gets a bumper payday in the third round, they might get TV as well.
"And there's 24 teams left over from the Premier League and Championship. You can still get Arsenal against Liverpool if that's what you really want.
"But what you really want is for lower league and non-league sides to have their moment in the sun, to have their big pay-day. Because at the end of the day, the big clubs are only there because of the grassroots clubs."
The former Sky Sports Soccer Saturday presenter, who replaced Laura Woods on the Breakfast show will present on Monday and Tuesday mornings.
Meanwhilem, Alan Brazil will take the reins during the rest of the week, with the show kicking off as normal at 6am.