New businesses are EXCITING!!! And the little details like the Taxes seem to just creep up on you in the midst of everything else. Here are some general responses, but understand that your specific circumstances may vary so don't treat this as gospel.
Who to file with - BOTH the state and the IRS. Prepare the federal return first, then use that information to prepare the state return.
What form to use - it depends on what election you made when you got your EIN. Partnership is Form 1065, S-Corp is 1120S (and 2553 if not already filed), C-Corp is 1120. This information will be on the letter you received when you got your LLC. Depending on which forms apply, the taxes were due either mid-March or Mid-April so they'll be delinquent. Very likely a penalty will apply but you can request that the penalty be waived if you meet the criteria for doing so but you have to ask for it and specifically identify how the entity meets the Rev Proc 84-35 provisions.
Regarding the capital contribution (money you put in), that also varies based on the method used so there's no clear cut answer until the details are clear as well.
Now a word of advice. You're taxes are late and there will likely be penalties. In addition, what you file this year will set precedent for future years. You may want to consider having a tax professional prepare the taxes this year then consider doing them yourself in the future. Better to get it right now than have to fix it in the future.
Your question is not something that can be easily answered on this board. As the previous attorney mentioned, the forms you will use depends on how you elected to be taxed. This goes for both the IRS and Michigan.
Regarding the money you put into the LLC, it sounds like you have a great deal of confusion surrounding the preparation of the tax returns and will likely need professional assistance.
We are a Michigan based tax law firm, feel free to give us a call should you need any help preparing and filing you Fed & MI State returns.
Too many variables to answer this question. However, from what you have said, this would not be a 'do it yourself' project for you and a professional should be hired. Don't hire someone who promises you a 'big refund'. Hire a professional and pay the professioanl fee for long term savings.