It is a good idea for bookkeeping purposes, especially if you have different investors, partners, or lenders on the different properties.

As for real estate software, I used QuickBooks for bookkeeping, that's about it, and I've been doing it for 40 years. 

Just a bit of advice and take it for what its worth, I am a lawyer with a master's degree in taxation and I have a book keeper who has her CPA and I have a CPA who handles our tax returns.

To do everything by the book while maximizing my tax benefits, some questions that I have about this are:-Should I keep separate bookkeeping logs for the rental side of the house and the unit I'll be living in?

Any good software that will store your invoices and bills for bookkeeping?

I have a VA bookkeeper who updates and emails me QB reports weekly and I review my financials on a weekly basis.

I would say my biggest weakness is definitely on the bookkeeping side.

Not an accountant but I apply common sense on how I tell my bookkeeper on how to record it, after all, I know more about my business more than anybody else.

The smaller management company software packages also do not interface with the popular bookkeeping packages.  

Receipts for expenses are managed using multiple shoeboxes to sort into various properties and categories and then handed over to my book keeper. :)Cheers,Ming