How can I stop TurboTax from combining my tax exempt interest and my ordinary capital gains.

[SteamTrain]

It doesn't if you enter the $$ in the correct spots on a 1099-DIV  (assuming that s what you are talking about)

When you enter a 1099-DIV form, Ordinary "Dividends" (plus short-term fund gains, box 1a) and Tax-exempt Dividends (box 11) show up on the menu page totaled together....but that has nothing to do with where they are used on your tax file itself.  

You did enter the total shown...whether taxable or not taxable is dealt with on the actual 1040 tax form.