Yeah, PayPal is awful. I used them my first year and had multiple hiccups. Eventually switched to Quickbooks and have been much happier.
If you're optimizing for cost (as opposed to speed), a lot of the biggest accounting software offer ACH transfers through their invoices. This is a free way to receive digital payments instead of paying processing fees.
Just be aware: with ACH transfer it takes longer for you to receive money, so you should expect about a week between getting paid and actually seeing the money in your bank account. But to some, this beats giving up some of your paycheck.