If you have multiple LLC's, then you will have multiple bank accounts, multiple tax ID numbers, etc.  The problem is not with the income/expense side, which can be easily split across several tax returns.  The problem is with the balance sheet.  It would be difficult or impossible to know exactly which assets/liabilities relate to which LLC.  This is called "comingling" and it generally should be avoided as it can lead to errors when a property is sold or disposed and an incomplete or incorrect set of assets/liabilities are removed from the books.

So I would say one QB company file per entity.

I would recommend a consultation with an atty regarding a single or multiple LLC's.  LLC is an asset protection strategy, and it can be void if you don't run the LLC correctly and/or comingle.  I've seen some bad outcomes. 

If you choose to use a single entity for multiple properties, then using the class feature is the way to go to simplify the profit/loss reporting.  You will also need to pay careful attention to the balance sheet fixed asset section to keep the asset cost basis straight.

Holler if questions.

Mark Wagner, CPA