Should a SIMPLE IRA be filed under a Traditional IRA in turbotax, or should it be considered separately since it is both individual and employer funded?

A SIMPLE IRA is, as you know, not just an IRA. You can make contributions to it only if you have a Schedule C - a sole proprietorship.

On the "Let's gather your business info" screen (the very first one), at the bottom under "Less Common Business Situations", look for Self-employed Retirement. Step through the screens carefully, because SIMPLE IRAs and Keogh plans and SEPs are all together here.