If you're asking if you should file Married filing joint or married filing separate; it's nearly always advantageous to file jointly. This doesn't change because you have a business. Also, there are numerous considerations besides taxes, for legality and other aspects, which I can't advise on.
When it comes to how to file taxes for a LLC, it depends on how many "members" (owners) were listed on the LLC paperwork with the state the business is formed in. It sounds like only one spouse is the owner; so it in this case, the single owner LLC defaults to being self-employed. This is easiest option and allows the owner to report the business on the personal return, with schedule C (attached to form 1040).
The spouse payed as an employee; the business should treat as an employee and issue a W-2 for. Then, the W-2 will also be reported as a deduction for the business (on schedule C attached to the personal return) and income on your personal return (by entering the W-2). The business will need an EIN for paying payroll taxes. These taxes are done separately from income taxes.
This means you can file your income taxes using TurboTax Home and Business. If you're both members of the business, it doesn't matter that one spouse takes a draw; that's disreguarded for tax purposes and the business net income is taxed. For more on this situation, see my explanation here: https://ttlc.intuit.com/replies/6081641
Let me know if you have any follow up questions.
