I have a 1099-SA which has two sections of information. It seems they are from two different Funds, do I enter this data as 2 different 1099-SA forms in TurboTax or as 1?

Which two sections do you have on there?

On the same one-sheet form it has what seems to be two 1099-SA forms, it has 2 boxes No. 1, 2 No.2, etc.; the amount in box No. 1 is different between each other; also, the box used for the Fund & Account number is different, where the account number is the same but the Fund code is different. Never seen this before in a 1099-SA.

Okay, you will need to enter those separately as if you have 2 1099-SA. So see my steps below. Let me know if that helps.

Thanks!

You will need to go ahead and enter those separately. You can use the instructions here to help you get to that section. 

1. Open your return and click orange Take me to my return button
2. Type 1099-SA or 1099SA in the Search box in the top right and click jump to 1099-SA or jump to 1099SA.
3. On the Tell us about the health-related accounts you had in 2016 screen, check the boxes for the types of accounts you have (these may already be pre-selected based on earlier info you entered).
4. Click Continue and follow the onscreen instructions to complete the form.

You will just repeat these steps to add the other separately. Once you have entered the first one and then jump to 1099SA again, you will choose the one you have and on the next page, click +Add Another 1099-SA and enter the other information.