Hi @ianjh
Generally for every PayPal transaction in, there’s another 2 out.
For example, if a client pays me £100.00 via PayPal, PayPal then takes their cut (I believe 3.4% + £0.20 as standard), and then pays me the rest, in this case £96.40.
So, the PayPal account would have the following 2 transactions created:
IN >> £100.00
OUT < £96.40
The In transaction you would tag to your invoice as you normally would with your normal bank account (say, with a incoming bank transfer, cash in, or a cheque etc). Then your out transaction, in this case £96.40, you would tag as a bank transfer to your main bank account - this would be when PayPal deposit the money into your bank account.
Just to spice things up a bit, you’ll notice that you’re then left with £3.60 sat in your PayPal account, which you would enter as a money out transaction, and tag it to a supplier called ‘PayPal’ and to the nominal code for Bank Charges.
In summary, for £100.00 paid in to PayPal, you would have:
IN < £100.00 (tagged to invoice)
OUT > £96.40 (tagged as bank transfer)
OUT > £3.60 (tagged to purchase invoice for supplier PayPal, and nominal Bank Changes).
And that’s that.
Sales Commissions, I would do the same if they’re paid by PayPal, either create a client record for each, or a general client called “Sales Commissions”, and tag to the Commissions nominal code (4902).
Hope that makes sense 
There’s also a Knowledge base guide here: http://help.quickfile.co.uk/main/1/how_do_i_handle_payments_from_an_online_payment_provider_like_paypal_.htm