There are two says and yes both increase jobs of the accountant for the reconciliation.
Using Bank Statement
You can import the invoice which paid through PayPal account (of course depending on the number and not based on the amount). For each invoice payment you have add one more line to the bank statement as below
(Invoice amount is 9705.00)
02/19/2014 / SO001 Agrolait Customer 120000 Accounts Receivable 9705.00 Create
02/19/2014 / SO001 Agrolait Customer PAL PayPal Payment Processing Fee -5.00 Create
And on the confirmation of the bank journal it will post below entry to accounting system
X 02/2014 02/19/2014 / SO001 Agrolait 101002 Bank BNK2/2014/0001/2 0.00 5.00
X 02/2014 02/19/2014 / SO001 Agrolait PAL PayPal Payment Processing Fee BNK2/2014/0001/2 5.00 0.00
X 02/2014 02/19/2014 / SO001 Agrolait 101002 Bank BNK2/2014/0001/1 9705.00 0.00
X 02/2014 02/19/2014 / SO001 Agrolait 120000 Accounts Receivable BNK2/2014/0001/1 0.00 9705.00
Second method is creating a Customer Payment Voucher as below
Choose customer select the bank account, enter the amount which exactly you get in to the bank like 9700 and manually select the full payment on the line which appear as below
SAJ/2014/0001 (SO001) 120000 Accounts Receivable 02/19/2014 02/17/2014 9705.00 9705.00 Y 9705.00
Also select the below options to do a full reconciliation for the customer.
Difference Amount : -5.00 â¹
Payment Difference : Reconcile Payment Balance
Counterpart Account : PayPal Payment Processing Fee
Counterpart Comment : Payment Processing Fees
And it will post the below entries which is far better then the entries created using the Bank statement
*10 BNK220140002 02/19/2014 Agrolait PAL PayPal Payment Processing Fee Payment Processing Fees 5.00 0.00 Balanced 0.00
*10 BNK220140002 02/19/2014 Agrolait 120000 Accounts Receivable SAJ/2014/0001 0.00 9705.00 Balanced A2 0.00
*10 BNK220140002 02/19/2014 Agrolait 101002 Bank / 9700.00 0.00 Balanced 0.00
If you work with the bank statement you need to do reconciliation manually, while vouched does automatic reconciliation when you confirm the voucher.