<UPDATE> The issues described below seem to be fixed. Using the Enigmail menu is a bit different from using the buttons and requires getting used to, although it is quicker imho. It would be nice, if the "Per-Recipient Rules" also supported S/MIME, to specify PGP or S/MIME based on the recipients address. <UPDATE/>
The version 2.0 really breaks interaction of S/MIME and PGP. In earlier version it was possible to individually set how to sign and encrypt mails. Now you can only turn signing and encryption on or off and "Enigmail will chose between S/MIME or OpenPGP depending on whether the keys for all recipients are available for the respective standard", whatever that means. And unfortunately, it doesn't work properly and is completely intransparent. This is a problem if you have both SMIME and PGP set up for one account. You cannot choose which keys to use for signing or encrypting. I also found, that SMIME is not used anymore if you also have PGP setup. Even if both sender and recipient also have SMIME available. So it's unclear how it actually works. Also, if Enigmail does not find a recipient's key, it will also not sign the mail, even if sigining is enabled.
Anyway, you can't set what method to use, you can't see, what Enigmail will actually use, you can't even be sure, that any signing or encryption ist performed at all prior to sending. That makes the whole thing practically unusable. Thats especially annoying since this extension seems to be the only one to bring PGP to thunderbird.
Until this behavior is fixed, you need to find an alternative mail client for encryption, which is extremely unfortunate.
This review is for a previous version of the add-on (2.0).
Please try the following build which should fix the issue with the default values: https://enigmail.net/download/nightly/enigmail-nightly-enigmail-2.0-branch-all.xpi
You can see what Enigmail does by checking the "Sign" and "Encrypt" icons in the toolbar. If S/MIME is used, then the status bar displays the S/MIME signing/encryption icons. In addition, the Enigmail menu tells you which algorithm will be selected and allows you to manually pick the algorithm you want.