Not sure I understood it correctly, but here goes.. So with your current joint bank account situation, your wife doesn't appear to be using it other than to transfer a fixed amount into it every month? IF that's the case, even if both of your names are on it (are they?), that's not considered a joint bank account in regards to what USCIS wants to see and won't help anything in regards to proving co-mingled finances. With joint checking bank accounts they want to see both of you actively using it, spending money via it etc. If her only relation to that account is putting a fixed amount of money into it every month, and not using it in any other way, that doesn't really prove anything. To USCIS, that could be her just paying off a personal loan she got from you, or her being your room mate and paying her part of the rent that way, or whatever. It doesn't help proving a bonafide marriage.
Do you have savings accounts, money markets or other financial "savings" in both of your names? If you do, send proof of that.