I'm guessing your kit was a Yankee Modelworks/Blue Water Navy. Iron Shipwright also makes an Atlanta-class cruiser, but ISW kits are typically whole hull.
YMW kits often have a mismatch between the upper and lower hulls. This is most often due to the differential shrinkage of the thinner hull bottom and the thicker upper hull & superstructure.
I've had some success in attaching lower hulls to YMW kits by using epoxy as opposed to superglue. The epoxy allows you several moments of free-time to position the parts before it sets.
Mike Ashey in his Kalmbach book "The Basics of Ship Modeling" has a more drastic approach. He cuts a mismatched lower hull apart - jigsaw fashion. Then cements the individual parts together. He fills the gaps with poured resin.
Essentially it is something you need to try and see what works best for you.