Here's what I do - it's probably odd, but works for me.
After every sale, I deposit the money into my business BANK account. I always leave a ZERO balance in Paypal. I like it clean, like that. I use only my biz bank acct for everything Etsy.
So, when I pay my Etsy bill, I do it from Paypal which is ZERO, but my Paypal takes it directly out of my biz bank account. I therefore only have one set of books to keep. I list everything in one check register.
It works for me. . .