The maps can be separated with permissions within one workspace, they don't need to be accessible (or even be seen) by everyone.
To move the maps from workspace A to workspace B, please follow these steps:
Make sure that you are an Admin of both workspace A and B.
Moving a story map, step-by-step:
2. Open workspace A
3. Open 'MANAGE WORKSPACE' menu in the top-right corner and select Manage storymaps
4. Click on the Options menu on a story map's tile
5. Select Move from the menu
If the Move menu is missing, please check step 1.
6. Select Move to B workspace
7. Repeat 4-7 with all the maps
8. Go to workspace B
9. Open the moved maps and 'Share' them with the appropriate people in the new workspace. You might need to invite them into the new workspace.