Managing the Assembly Structure in IRONCAD is as easy as dragging and dropping icons in the history tree! Just hold down the left mouse button on the icon of the Assembly/Part, or even a Feature within a Part, that you want to move and drop on the position you like.
Creating new Assemblies can be done even on individual Parts and Assemblies - the control is completely yours! Then add more objects to the Assembly by drag and drop.
The BOM will primarily look at the order of the items in the Scene Browser for the order of the items in the BOM list, but this can be controlled by a setting and reordered in different ways later. The Position order of the BOM also reflects the number shown in the Item Bubbles.