Hello,
For a stereo solve you would have 2 Markers (1 under each left/right camera), and single Bundle with both Markers linked.
I don't think the Load Markers tool automatically links
To link multiple markers and bundles, use the "Link Marker and Bundle" tool:
An example setup is here:
In the screenshot above I have deleted the second bundle ("bundle2_BND"), renamed the markers, and then re-linked both the markers to the same bundle.
Also, in the example I have the right camera under the left camera. This allows you to solve the secondary camera relative to the left (hero) camera, and you can solve offsets for the right camera, as you need.
Other than the Markers and Bundles being linked, if you are only solving an object, there is no extra setup that I am aware of.
David