It's not uncommon for a business to have more than one account. For example, your bank account where money is deposited, and a credit card used for business expenses.

Wave will dump all your accounts into a single list of transactions. Although it tells you which account each line belongs to, this combined list was not built for easy understanding.

Even more confusing with Wave is trying to reflect a transfer between your accounts (ie: paying off your credit card from your bank account). The process seems counter-intuitive and, especially if your banking data is not able to automatically connect, this simple action can be a real headache. Even I was yelling at my screen the first time I encountered this.

QuickBooks handles your bank feeds by having separate lists for each account. Visually, it makes a lot more sense. It will also allow you to make transfers between all your accounts, and often is able to automatically find the corresponding transaction. From that perspective it's an easier system to use.

Another important piece of recording your bank transactions is matching them up to your bank statement (called reconciling). If you're not doing this monthly there's a risk your books will be incorrect. Wave doesn't have a built-in area to do this, but QuickBooks does and it's very easy to use.