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You're better off getting a better audio interface and connecting them all to their own line ins. If you have a 2 in soundcard, everything from the mixer is going to come through that, meaning you can't eq/compress/do anything your synths independantly in software - you'd have to do it all on the mixer, which is usually crap unless you're spending tonnes on a proper console.
Regardless, there is no reason why it wouldn't "work" with FL - all FL has to do is accept audio in on one of its mixer channels.
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