1. Line up your objects in Composer.

Lining up the objects in Composer is necessary so the Bank Tool will bank both objects evenly.
Below I lined the two ships so they will bank the same when either one is unmasked. Remember to leave enough space between the two so they cam be masked separately.

Front View

Side View

Top View

2. After merging ( I delete the two original objects ) then go to mask and mask one of the objects and move it to the desired location, using the mask Displacement Tool. Note that when using The Mask Displacement Tool it is the mask object that is effected. The invert the mask and move the other object.
Below I moved one ship so far forwards it's off the screen, and the other so far back it's not visible. Then go to Composer and set the first keyframe.

Keyframe 1

Repeat step 2 and set keyframes until you have the effect you desire. Most all the tools in Tools & Distortion Can be used on each object separately, by masking one and using the mask invert tool to switch between objects. The Rotate Tool will not recognize mask, so it manipulates both object together when used.
Below I moved the 2 ships closer together and set another keyframe.

Keyframe 2

3. Then with one ship masked I used the Bank Distortion Tool, and rotated one clockwise. Then inverted the mask and banked the other counter clockwise and set keyframe 3.

Keyframe 3

4. I made the ships pass each other barely missing, then banked them back level, then set keyframe 4. Since all the motion is calculated between keyframes it was important that I put enough distances between the two ships before banking them back level, so they wouldn't level out to early and pass through one another.

keyframe 4

5. Them I moved one so far back it disappeared, and the other so far forward it went off the screen and set the last keyframe.

>Keyframe 5