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How do I set up Quickbooks for a small property rental company that holds its properties in separate LLC's? 
You need one "company file" for each company that you want to track through QuickBooks.  Looks like, in your case, that is at least the PM and the PH (as you labeled them in your question).  The companies that just hold property and pay utilities might be simple enough that you don't need the full power of QB, in which case you might just track their finances on a spread sheet.  Subsidiary companies will probably appear as "assets" of some sort on the books of the parent company. This set-up probably does limit liability at some level, but it's going to create a lot of overhead for your that incurs some expense either in your time or in actual fees paid.  You should really consider whether the limitations on liability balance against those costs. (Think ahead to what you're going to do when you have to file taxes on this network of companies, whether you need separate insurance policies for each instead of getting one policy covering multiple properties, etc.)