How do I make a Sale which has been Paid (not deposited) deposited? Also how do I account for the fact that the deposit is less than the sale because of Paypal fees?

I'll help you record the transactions, claire10.

We can use the sales receipt to record the sales and deposit it to the Undeposited Funds account. Then from the deposit section, we can deduct the PayPal fees. 

To create a sales receipt, you can follow these steps:

1. Click the Plus (+) icon located in the upper right corner.
2. Under Customers, click Sales Receipt.
3. Select the customer's name, and choose Undeposited Funds from the Deposit To drop-down list.
4. Enter the sale information.
5. Click Save and Close.

Once done, let's create a bank deposit and add the PayPal fees.

1. Click the Plus (+) icon located in the upper right corner.
2. Under Other, click Bank Deposit.
3. Put a check mark on the customer payment.
4. Under Add funds to this deposit, choose the customer's name from the Received From column.
5. Choose the PayPal account or create an expense account for your PayPal fees from the Account column.
6. Enter a negative amount in the Amount field.
7. Click Save and Close.

I've added some screenshots for reference.

You can always visit us if there's anything else you need with QuickBooks Online. Thanks.