Personally, I don't have a strict budget, but I do carefully track spending each month. I don't have a policy of lending anything to anyone and expecting to get it back. All "loans" are gifts as far as I'm concerned, so I put down the full amount when I spend it, and add the repayment back in if/when I'm paid back. For credit cards, I also count the spending in full when I charge it on my card. If it's a big ticket item I have been saving up for, it'll have its own budget line and will go against that. If it's not a big ticket item, then it's a routine purchase and it'll get paid off at the end of the month as if I'd paid cash anyways.
In my opinion, all spending is cash out the door - it doesn't matter what method you used to spend it. My spreadsheets are set up with that in mind though, so do what works best for you. It's your budget, so you can set it up however it helps you save money and track your spending.
As for apps, the Mint app works fine for me but I do most of my actual expense tracking on a desktop computer.
