How do you reconcile Invoice charge to $ actually received?

I assume this is using the Quicken "business" version as I understand there's an "invoicing" process associated with that version.

To maintain accurate accounting records you must make some sort of accounting entry in Quicken to recognize that expense, you can't just ignore it.

If you can calculate the Stripe charge at the time that you create the invoice then ideally you'd like to incorporate that charge at the time that you create the invoice.  That is, the process of "invoicing", which is the moment that you recognize the revenue, would create an accounting entry like this:

Debit (increase) Accounts Receivable (an "Account")   $146.55

Debit (increase) Stripe Processing Fee (a "Category")     $ 3.45

Credit (increase) Revenue (a "Category")                                      $150.00

That entry recognizes the revenue ($150.00), the expense ($3.45) and the net amount you expect to receive ($146.55).

Then when Stripe processes the customer's credit card and deposits the net amount into your bank account the Quicken entry would be:

Debit (increase) Checking (an "Account")                           $146.55

Credit (decrease) Accounts Receivable (an "Account")                     $146.55

clearing out the receivable and showing the correct net deposit in the checking account.

Since I don't use the business product I don't know if Quicken's invoicing process is capable of doing that.  You'd want the customer to only see the $150.00 charge to him, not the Stripe fee.  Perhaps someone who actually uses the business version can chime in here.

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ASSUMING, for the moment, that the invoicing process can't do the above accounting, then YOU have to edit that $146.55 deposit into the checking account to get the accounting to work properly.

That is, you'd make that $146.55 deposit into a "split" entry in Quicken.  The split would have two lines:

Debit (increase) Stripe Processing Fee (a "Category")     $ 3.45

Credit (decrease) Accounts Receivable (an "Account")                     $150.00

Mechanically, you'd enter the $3.45 amount as a NEGATIVE number in the split window.