Attaching top to bottom?

This seems so simple, but I'm clearly missing something fundamental. The hardest thing for me on every model I have built is attaching the top to the bottom in the final steps. The bodies always seem slightly warped, so they need glue, but there is nowhere to glue to. What's the proper method?

Hi Marlin,

Can you tell us which kits you've been having problems with? There's so much knowledge here that someone else is bound to have built the same one.

Presently, it's the Tamiya XJ220. The Revell Premium 560SEC I built was also very bad in this way.