Filing joint does not change the fact that you are the one and only owner of your business. You will still report all business income/expenses on SCH C as a physical part of your joint tax return.
However, mxing business money with personal money in the same account tends to create a book keeping nightmare. From the sounds of it though, I get the impression that you've keep detailed records and can therefore justify and prove all of your business transactions if ever audited on it.
But for the future, starting today if not sooner you need to open a physically separate bank account for the business. Many banks now-a-days offer free business checking. So cost should not be an issue. I recommend you do as I do with my SCH C business.
I have a physically separate checking account for the business. It was my personal preference that I not have that account with the same bank where the personal accounts are. Any and all transactions for the business are run through that business bank account with no exceptions. When I get my bank statement each month, each and every single transaction on that statement is a business transaction. Period.
Once a month on the 1st business day of that month I take an "owner's draw" out of the business account and deposit it into the personal account(s) as needed. That is the absolutely only transaction that has anything to do with non-business each month. There are no others. Not ever. No exceptions.
I use Quickbooks for the business account. Makes life easy all the way around. It's a snap to balance my monthly statements each month, and at tax time I can import directly into TurboTax from Quickbooks. Saves me a ton of time.
I am also compensated by another company on a W-2
No big deal. Just enter the W-2 just like to you do your wife's W_2 and in the same section of the program. But do be aware of this: If your W-2 has the "statutory employee" box checked, then it's self-employed income and it's *IMPORTANT* you pay attention to detail so you make the right selections that will ensure it is included in your *EXISTING* business SCH C, and doesn't create a *NEW* SCH C.
