CC payment deposit adjustment

I'm in a bit of a bind with CC payments and I'm not sure if there's an easy way to fix this or not. 

We use PayPal for our CC processing. We typically get payments through checks but we do accept CC when customers need us to. But now a problem popped up during reconciliation.

The problem is this

1. Whenever someone pays with a CC my AR manager was marked them down as paid though Quickbooks on the invoice, like you regularly would when accepting a check payment but she didn't transfer the money into our bank until sometimes a month or 2 later. So it looks like it was paid one day but the money doesn't come into our bank for another month.

2. We aren't recording the fee associated with accepting the CC payment correctly either so the invoices that have been paid have been recorded without the fee so the when we actually do transfer the money from PayPal into our bank the numbers don't add up since whatever the original invoice costs is higher then the invoice minus the CC fee PayPal takes out.

I didn't know she was doing it this way so when I started the reconciliation I was matching up the PayPal transfers and having the payments go in the right accounts but now we are basically showing 2 payments for every invoice paid through CC. 

3. The PayPal transfer we make is in one lump sum so it's sometimes hard to see which invoices it's paying for.

Is there an easy way to fix this? Would anything bad come of just keeping the lump sum payments recorded the way I have been for the rec and just delete or void all the invoices paid this way or do I have to go back and manually enter the payments for the dates the money actually came into the account and alter the price of the invoices manually?

Thank you!