There are a number of options to consolidate your reports, which ultimately depends on the "layers" of reporting that you require. You can visit "File Structure" for various scenario's, however we can broadly classify the options as follows:

Use Divisions to setup multiple divisions within the file with each division being the respective entity. This will provide for 2 layers of reporting; Consolidated and Divisional.

You can view the reports by simply selecting the drop down filter in the top right hand corner with the "All Divisions" option being the consolidated report. You can exclude the inter-entity accounts under Chart of Accounts. 

Setup multiple files for each entity, add a group and then assign the files to the group. 

You can add a group under the "Organisations" menu item which is on the page that appears when you first login to Magnifi. There is a sub menu item called "Groups" and once the group is added you can then assign the file as follows under organisation details (select edit icon that appears next to the organisation name)

This will add a 3rd layout of reporting, meaning you can report by group, entity or division. The organisation flowchart which appears under "Add Division" (drop down at top of screen) will then reflect 3 layers as per following example:

If you are consolidating using the 1st option referred to above, you simply select the drop down in the top right hand corner of each screen to report by division or "all divisions" (being consolidation). You can exclude inter-entity accounts under chart of accounts which will exclude any values that appear within a division. This option allows you to view consolidated reports on screen or via excel and when you export to excel there are various worksheets that appear including a worksheet that will compare the divisions/entities. 

If you are consolidating using the 2nd option, you can export the reports to excel to view the consolidated report.  An option appears at the bottom of the relevant features (eg Actual v Budget) called "Export Group" and once exported, it will produce the consolidated report in excel with various worksheets including an organisation comparison.  You can exclude "inter-group" accounts under Chart of Accounts which will exclude any values that appear within an organisation. 

Under Chart of Accounts, you can exclude Inter Entity or Inter Group transactions from the Consolidated Reports as shown below;

Inter-entity will remove the divisional account values when you filter your reports at the  "All Divisions"  level.  

Inter-group will remove the organisation account values when you export the group report to excel.