The BIP39 passphrase option is disabled when creating a new wallet. This is on purpose because it is a dangerous feature for new users - the extra BIP39 phrase is NOT shown anywhere in-app, and if one forgets it the wallet cannot be restored with just the normal Recovery Passphrase.
Here's how to do it: (Instructions for single device)
1. Back up your recovery passphrase.
2. Click on .../Settings/Restore Wallet
3. Click on Create a new wallet
4. Get the new recovery passphrase, skip the password step, and add the wallets you would like to have.
5. Click on .../Settings/Restore Wallet again
6. Click on Restore a Wallet and enter the new recovery passphrase you got at step 4, but this time click on the extra BIP39 box and enter any phrase or word you like.
7. Enter a strong password.
8. Add the wallets you added in step 4.
(This is optional, but you are strongly advised to try restoring again with your new recovery passphrase and your extra BIP39 phrase and check that you are receiving the same addresses in all coin wallets)
9. Go to a couple of your wallets, swipe to the Receive tab, and note down/screenshot the receive address given by Coinomi.
10. Click on .../Settings/Restore Wallet
11. Enter your new Recovery Passphrase, click on the extra BIP39 box, and enter the BIP39 phrase or word you entered in step 6.
12. Enter your strong password.
13. Add the same wallets as in steps 4 and 8.
14. Go to the wallets you examined in step 9, swipe to the Receive tab, and compare the addresses with the ones you noted down in that step (9). If they match, you are good to go.
Then it is a matter of transferring your coins to the BIP39 passphrase enabled recovery phrase. To do this using a single device, you will need to:
15. Go to each of the added coins' receive tab, and copy the addresses.
16. Click on .../Settings/Restore Wallet
17. Enter your old, original Recovery Passphrase (the one you had before you started this process), and do not click the extra BIP39 passphrase box.
18. Skip the password step, and add the coins you had in your original Coinomi wallet.
19. Go to each of the coins' send tab, click on "use all funds" and paste the receive address that you got for that coin in step 15.
20. Click on .../Settings/Restore Wallet
21. Enter your new Recovery Passphrase, click on the extra BIP39 box, and enter the BIP39 phrase or word you entered in step 6.
22. Enter your strong password.
23. Add the same wallets once again.
You should now see all your funds in your new, BIP39 protected wallets.
Keep in mind that you can always keep using your plain recovery phrase wallet in addition to the BIP39 passphrase enabled wallet(s).
Remember that for one recovery phrase you can have many "hidden" wallets, each one of them using a different BIP39 passphrase. This will be explained and instructions on how to do it will be provided in another article soon.
The BIP39 passphrase is standard and it is supported on various Bitcoin wallets, but not all. Due to the way it is implemented there is a chance that it would not work if your BIP39 passphrase has composite letters, for example é, å, ώ (they can be interpreted as a single letter or a plain letter + a letter mark). If you want to be 100% sure that you are not affected from this and be cross compatible, make sure you check that you get the same addresses using the recovery phrase tool (it works even offline, just save the page). If you enter a BIP39 passphrase in the tool and you get the same addresses as in your Coinomi account, then you are OK and you will always get the same addresses as long as you enter that exact passphrase.
Final warning, be sure to backup your BIP39 passphrase somewhere safe, away from your device.