Let me help you or perhaps add to your confusion. A 2 member LLC is treated as a partnership but here is your salvation. An entity that would normally be treated as a partnership can elect not to be treated as a partnership if the income of the partners can be adequately determined without a partnership-level computation. This is what you have been doing and I would argue that you have in effect elected out of the partnership provisions by your previous filings. I would file as you have in the past and attach a statement to your return that "The members of the (Your LLC's name) are husband and wife and have elected out of the provisions of Subchapter K of the Internal Revenue Code since (insert the year you first filed)."
As you can see from the other responses Partnerships are extremely complicated and will require you to file a Form 1065 and Schedule K-1s for each partner - a daunting task for someone who is not a tax professional. I don't know why you are filing separate Schedule Cs for the same business unless you have some dire need to segregate all of your activities. My advice to a new business is usually to start a single member LLC for some protection from liability. Be sure you follow all of the provisions your state has to keep the LLC registered and treat it as a separate entity with separate bank accounts which you have done. One benefit of the LLC is that a single member LLC is a "pass through entity" requiring no separate return - you just pick up its income on a Schedule C. For some reason having one of you own the business doesn't work for you. I think electing out of the partnership provisions (Subchapter K) is the way for you to go or you will be headed down a difficult path. If you truly want to treat the LLC as a partnership find a tax person familiar with partnerships to advise you and do your return. I can't imagine a neophyte can do an accurate Form 1065 without a great deal of help. If you wish you can text me at [phone number removed] with your phone number tomorrow after 10:00 EST and I can fill you in on this as a favor. I don't know what state you are in or if your state has some rules that differ from the Federal rules!! Usually they are the same.
