Good day Romeo2244,
Congratulations on your new LLC! You have brought up quite a few items that we can cover one by one. As a general rule, you can find a ton of amazingly helpful information at the IRS Self-Employed Individuals Tax Center
1. When you filed for your EIN and LLC you would have received an SS-4 notice from the IRS. On that notice it will tell you what type of return the IRS will be looking for tied to that EIN. Depending on how your LLC is structured you might see a 1065 for a partnership or an 1120 for a corporation. Business Structures on the IRS can help explain some of the differences. You mention LLC and managing partner.
2. Your wife sounds like she is a W-2 employee. Often both active managing members and employees will be on the payroll. There are many different ways to do payroll and using your EIN to report the payroll is ideal. Video: Guide to Payroll Taxes
3. I am not sure I understand why you put both your wife's name and the business name on the checks. If they are her payroll checks they should go into a personal account not the business account. It is not a good idea to deposit individual payroll amounts into the business account.
If the checks are payments to the business for services rendered her name does not need to be on the checks at all. Keeping business income and personal income is one of the key aspects of running a business and is often a challenge for new businesses.
When you are starting or reorganizing a business there are many factors to take into consideration. Often the type of business you have, the number of employees you plan on having, and even the nature of the business can have an effect on your taxes.
I hope this gets you in the right direction and I am happy to go into more detail if you have further questions.
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