My second question is, since both of my W-2 reported my IRA (Roth & Traditional) investments, do I still need to put them under Deductions & Credits since I didn't get a tax form from them or no?
If you did not make any contributions to your HSA or your MSA other than through your paycheck, then you don't need to worry about your 5498-SA. This form is sent to you for information only. You will need to enter the amount on your W-2 in Box 12 with code W. You will not need to enter anything further about contributions to your HSA.
You will only get a form 1099-SA if you withdrew money from your HSA. These forms must be furnished to the recipient by January 31, so you should have gotten yours by now.
When you put money into a retirement account through work, you do not need to report it (assuming you meant 401k or similar). If you contribute to a retirement account outside of work, you need to report that, since there are restrictions on how much you can contribute.
Here are links to the various types of retirement plans.