Stripe Merchant account fees

Stripe Merchant account fees

Can anyone share with us how they are accounting for the specific, per invoice transaction fees associated with a credit card payment through Stripe?  
When we log into Stripe's Dashboard and open a particular day's deposit to our bank we see fees that have been deducted from that payment.  The problem is that some of the fees are from the previous day's charges and some of the fees are from two days prior.  Stripe does not show the fees associated with a single charge.
How does Books "know" to match an amount that comes into our bank and "take" money from the Stripe Clearing account (where the initial amounts have been accumulating)?
And why aren't there the Stripe fees listed anywhere in Zoho?  Back in 2018 (yes, we have been away from Books for several years), Books used to account for the fees associated with Stripe charges.
Did something change in Stripe?  Did something change in Books?  
We don't like the lack of transparency.  We have no idea what fees are really being deducted per charge.
We have reached out to both Zoho and Stripe and neither seem to want to help or are able to help.  We have a hard time imagining that we are the only customer experiencing this.
Should we consider a change to Forte?  Anyone have any experience with Forte and how their system works with Zoho?
Thanks!
Paul