I do not know about any automation methods with the amount of transactions you have, but this is the best way in my opinion to account for the paypal transactions in your financial software. The method I use works in quickbooks anyway I assume it will in the software you use. Paypal is essentially a bank account. Technically this is true. Create a bank account in your financial software labeled as "PayPal". Create an expense account named "PayPal Fees". Create a payment type as "PayPal". Record your sale as normal. In the sale use the full price that your customer paid for the items. Do not worry about the ebay fees at the moment. When you receive the payments in your financial software, choose the "PayPal" payment type. This way when you do the deposit it helps to keep you from accidentally depositing cash payments in to paypal bank, and paypal payments into your normal checking account. When you receive the PayPal payments also choose to deposit them into the "PayPal" bank account. Next is to decide how often you withdrawel paypal funds to your checking account. For example if you do it once a month, then you can export to CVS file all transactions after the previous withdrawal to current withdrawal. Use an excel formula to quickly add up all of the paypal fees. Using the "PayPal" expense you can record the total fees by writing a check from the "PayPal" bank account to a vendor you can create called "PayPal". Once I see the withdrawal is received into my checking account I will then do a bank transfer from "PayPal" to the "Checking Account" If you are making purchases or paying ebay seller fees using your account, then you can write checks from "PayPal" bank account. Either enter each payee as a vendor or create a general expense to write the check to. There are many ways to do it all.
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