Hi Mona3739,
When you set up online payments, you can choose to either pass on the customer surcharge by default for all invoices or only for specific ones. If you notice that some customers are being charged a surcharge and others aren't, double-check your default settings and the individual invoice settings to ensure everything is configured correctly. For more details, check out this link.
As for manually allocating payments, it won't affect your bank reconciliation, as long as you're selecting the correct account during the allocation process. For more info about payments and fees setting check it out here.
Cheers,
Princess
