I've no idea of the 'best' way, but here's how I do it.
Ebay -> Linnworks->MS Access->Transaction Pro Importer & then finally -> Quickbooks
and not an accountant in sigh in that chaint!
it looks long winded, bit it's not...one days worth of sales gets piped into Quickbooks at the end of the day (takes about 2 minutes to do about 60 transactions)....I've coded MS Access to allocate the VAT code for the transaction (based on shipping county)....then once the transaction arrives in Quickbooks, it calculates the VAT (no human intervention required). I can then instantly see in real time how much gross profit I've made that day, week, month, financial year etc.
I don't 'handle' paypal on a transaction basis ...basically the proceeds from all ebay transactions goes into a 'bank' (a holding bucket) that I've called paypal gbp within Quickbooks. I've also added paypal as a supplier....once a month I add their fees into Quickbooks as a bill & then pay the bill from the paypal gbp 'bank'
Like wise Ebay fees....add them as a supplier & pay them from the same 'paypal gbp' bank in Quickbooks.
Granted, it wasn't the easiest to set up, but it's one of those win things...spend a BIT of time to save a LOT of time....what used to be my biggest headache & time sump is now pleasurable!
if you think Ebay is a headache wait until you use Amazon FBA....you'll spontaneously combust at the mere thought of having to wrap your head around the way they do things!
(BTW pointless asking accountants how to handle things like Ebay & Paypal...this is a process thing vs. a pure accountancy thing - best asking on an ecommerce forum)