I received my answer from Derek Krebs of the MSX Group, as follows:
First option, you may log into company 1 as the default in Mgt Reporter and build the tree on all departments (in tree under Edit | Insert Reporting Units from Chart of Accounts). Save the tree and File | Close All then log into company 2 (Company | Companies, choose Company 2 then Set as default). Open the tree you saved before then go to Edit | Insert Reporting Units from COA which will add Departments for Company 2 to the bottom of the tree.
Second option, simply copy all of the Department tree units from Company 1 and paste at the bottom of the tree then change the Company (assuming the same Department numbers and descriptions, find/replace selection or copy/paste).
In both cases, you can easily create new summary units in the tree by right-click Insert Reporting unit in the worksheet view to the right within the tree then in the graphical view to left you can either Promote/Demote units or drag & drop.