The journal you are planning to submit to will have all of the formatting information in the author instructions (usually including what they want the tables to look like). If you haven't settled on one journal yet, you can pick one you think you might want to submit to and format based on their requirements (you might need to reformate later if your decide to submit elsewhere but that is easier once the paper is written). It also helps to look at papers similar to yours (i.e. if you are trying to publish a case report, look at case reports in your target journal) and see what they are including and how they are structured. That can help guide you early on.
As for pulling references, use your school's library to access papers. Google Scholar can be a good starting point but it has issues and can't be relied on. Citations are always available to download either through google, the repository, or the publisher's website. I would use a citation manager (Mendeley is free and integrates with Word). If you don't know where to start, ask a librarian. They can show you how to use the resources the school gives you. Also if you don't have access to the full text of a paper you need, you can usually request an interlibrary loan and get a copy.
Making tables and figures can be hard. Decent tables can be made in Excel (and/or directly in Word these days). As long as you don't just use the default ugly formatting, that is the best. Figures are harder to make and there are a million ways to make them so that you would need to decide based on your research.
Some general tips:
1) Take your time reviewing the literature - be thorough. This isn't a college essay where you just cite the first few google results that match you search. This will help avoid any embarrassment in your intro and discussion.
2) Have people read the paper. Your advisor will, but other faculty can provide good insights. Ask around, people are usually willing to help if you ask nicely.
2b) If someone reads it and says "wow this is great as-is" find someone else to read it. Your paper will need editing. Don't be afraid to rewrite. This isn't a commentary on your writing skill or anything. Everyone needs to revise their papers. Once you think your paper is done and ready to submit, set it aside for a week or so and then come back and do a final pass.
3) Have discussions about author order early and often. Even if it's just you and your mentor, it's a good habit. I've seen a lot of drama resulting from not addressing authorship until the last minute.
4) Use a template and follow the author instructions of your target journal. It's annoying to go back and forth with the editors office fixing stupid formatting issues.
5) Don't worry! As long as you don't lie, plagiarize, or commit some other form of academic dishonesty, nothing bad will happen. Mistakes are not the end of the world and if you are diligently checking your work, you'll catch any before the paper goes out the door.
