Yes, you will want to file Married Filing Jointly and include you wife's W2 and 1098T on the return.  She should also receive a 1098E for the interest she paid on student loans.  TurboTax will ask you if you have had any life changes, such as getting married.

I just finished filing my wife's and I W-2s, 1098s, and other documents. I just found out that i had a 1099-SA form i forgot to file. My federal and state return was accepted and now i am awaiting payment. Does this form make a difference whether or not i file it? and if so, how hard is it to file an amended return on TurboTax online? when can i do this?

Now that your return as accepted by the IRS you will have to wait until your taxes are fully processed and receive your refund Then you will have to log back into your return and and enter your 1099-SA.

You will then amend your return by entering the form 1099-SA. The amended 1040-X will not be available until mid-February.

Form 1040X can't be e-filed per IRS regulations.

After you finish amending in TurboTax, we'll guide you through printing and mailing your 1040X along with any required attachments.

Three weeks after mailing your amendment, you can start tracking it at Where's My Amended Return? on IRS.gov.