Currently use YNAB and it drives me bananas. The way it refuses to reconcile budgeted money for a CC against the interest/fees for that card as monthly payments often go out BEFORE interest is assessed for the month, requiring a convoluted interest bucket and juggling. I'll give this a shot.
The way I treat interest/fees is as just another expense. Then there's no juggling. But I manually enter all the transactions, I don't know how this works if you automatically get transactions, as it would depend on how the CC or other companies add interest onto the statement (as a regular transaction or separately). So once a day (typically, at least 3-4 times a week) I go into each account and YNAB and make sure everything is present. If interest or fees are present, I add those as transactions. YNAB properly accounts for it (if you budget money into the interest/fees categories) for the next CC payment.