If you are plugging the stereo outputs of your keyboard into two line inputs - and pan one fully left & the other fully right - you should get the same results as plugging into the stereo line-in.
Plus, you may benefit from the EQ controls on these inputs that the CD input probably doesn't include.
Depending on how the FOH speakers are placed in the room, you may want to try panning each input closer to the middle to hear if that sounds better.
Experimentation is key to getting the best sound.
Good luck.
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