I use Mint.com to track expenses. While it is not the only automated system available, it is one of the most widely used and the price is right (free). That being said, I have a bit of a love / hate relationship with the program. I don't like being bombarded with advertisements and irrelevant recommendations, but it captures all of my monthly transactions across multiple accounts and provides clarity on our household spending versus our budget. Here is how I use it: Weekly: I log into Mint and let the accounts update (this takes a few minutes). Once they are updated, I go to "Transactions". View recent transactions and confirm they are categorized correctly.
Monthly: I go to "Budgets" and see how we did with our spending in various categories versus the budget. I focus on discretionary items like eating out and shopping since our mortgage, car payment and utilities don't really change month to month.
Monthly: I go back to "Overview" which is the homepage. Scroll down to the lower left-hand corner to view the Net Income chart. Make sure you are earning more than you are spending. If your goal is to have $1,000 / month surplus, the net income should consistently show around that amount.
Do not upload business accounts to Mint. Keep them separate for accounting and cash flow purposes. I use Quickbooks Online for business accounts and find it easy and effective once it is set up.
Other solutions I have heard of: You Need a Budget (YNAB), Toshl and Mvelopes. What system do you use? Email me at firstname.lastname@example.org.