I have multiple LLC's that are 100% owned by another LLC, each with their own instance of QBO. How do I consolidate these to generate a single tax return?

Is the top level LLC filing a 1065, 1040, or 1120S or 1120?

What activity(ies) are the lower level LLCs? 

We have this situation too with a holding company that supports several SMLLs which hold commercial rentals.  We set these up in QBO with Class (Location) codes for each SMLLC. This way, you can print and export the consolidated results. When you need separate entity information, you can pull P&L and Balance Sheet reports that show the classes.  Works great for income, not quite as easy for the balance sheet.

When we need separate reports by entity, I export the reports with Classes to Excel and then hide the columns I don't need. 

When we set up on QBO, the Class codes didn't attach to the opening balances (e.g., bank accounts).  Not sure whether this was our set-up contractor or the system but I can't add class locations after the fact for the opening balances. So we have to manually add the historical opening balance to the ending balance in QBO to get the correct ending balance that ties to the bank.

Since these are SMLLCs, I'm not worried about the separate equity section.  Like the bank accounts, the equity section needs to be summed together and reconciled if you make distributions from the LLCs to the parent company.