"However when I get a credit and enter the credit toward the bank account (only choice) it seems to work OK."
It is not your Only choice; you get expense and items tabs in the Credit Card Charge screen, the Credit Card Credit screen, checks, vendor bills, vendor credit.
That would not be correct, if the Credit Card Credit is due to a refund On that card as a return, say, of a Toner Cartridge. That credit is listed as Office Supplies on the Expenses tab of the Credit Card Credit.
You would put the Credit Card Credit to Bank on the Expenses tab to reflect a Credit Card Balance Payment was made from Checking.
"But when I reconcile I see these credits showing up in the left pane of charges and I don't know if it's normal."
If you can reconcile, you are fine. That is the point of reconciliation. In your example, you would need to be expecting this in Credit Card reconciliation and in the Bank reconciliation; if that is not what was supposed to happen, you entered this refund incorrectly.
