Here's the long version. For the short version, skip to the second to last paragraph of this post:
The theory behind YNAB is that you give ever single job a dollar, so everything is accounted for (even wild hair money).
For example, a paycheck you get from your day job might be entered into the register as “income available for November.” You then assign each dollar from that paycheck a job: $900 to your mortgage, $200 to utilities, $150 for dining out/entertaining, $50 for blowing wherever you'd like, and so on. Until there's nothing left on the table. Prior to assigning dollars, you've estimated what you need to spend on each category each month.
In the same budget, you might have a grouping of categories for a rental property. When you receive your rent, say $900, instead of that being set as “income available for November” it would be allotted to $400 for mortgage, $120 for taxes, etc.
When you incur an expense, whether personal or for an investment, it gets put in the register (just like in Quicken or similar programs). You can see how much money you have left after you've categorized it against what you've budgeted, or in the case of other categories, how much savings you're building towards a repair or upgrade for a property.
If you overspend, the amount is taken out of the next month's available balance, leaving you to make it up by spending less in whatever categories you choose. If you've underspent, hopefully you've allotted that money to a savings category, otherwise it rolls over to income available for the next month. Each dollar always accounted for in some way.
The other idea behind YNAB is to get to the point where you are living off last months income, which can come quickly to some or take some time, depending on where you are. This holds true for rental properties as well as personal expenses. Once you have a clear idea of how much you spend each month, you might start allotting an amount out of each check or windfall towards the rainy day fund. Dave Ramsey has a similar approach, but I believe he works towards having just $1000 stashed. A lot of people on the YNAB forums seem to have started with Ramsey's approach, and then moved on to this one.
This may seem like no-brainer stuff to number crunchers, but to the more creative types who struggle with managing their money and investments, I think this is the way to go.
Also, their forums are stellar. Fast and responsive, and just as positive and supportive as the BiggerPockets.com forums. People who use this system are passionate about it, and they are more than willing to help you along.
How has it changed my life? In my wild youth before kids, property and responsibility, I was never good with money, didn't get how to budget. Always worked in fields where I had plenty to play with (relatively speaking), so I didn't worry so much. I tried standard budgeting, but it always seemed like you were asked to set a budget and then live within it. I didn't get it (I was an English major). If I didn't get the numbers right when I was putting together the budget, I was always behind the eight ball either feeling like a failure or just giving up on the whole budgeting idea and leaving it behind for a stab at it another time. With YNAB, you can see exactly where your money is going, where you need to spend more or less. Its all right there. No judgement.
As a result of using this program, money is no longer a mystery to me. It also removes the purse strings responsibility if you are living/working with a partner, since everything is right there. I also use it for my kid's allowances, and they can track how much they have, what they've spent money on. It helps them to understand how quickly money vanishes if you don't spend it with care.
Told you this was the long version.