Yes, your existing Multireddits will appear in their alphabetical place in your subreddit list in BaconReader with a tilde "~" next to them, indicating they are a Multireddit.
To create a new Multireddit from within the app, from your BaconReader subreddit menu select "Manage" then on the Subreddits page, tap "Multi" then "Add Multireddit."
Pick a name for your Multireddit - I'm going to create one for "guitarstuff" (no spaces are allowed as Multireddits must meet subreddit naming conventions).
Once the Multireddit name has been entered, if you wish to make the Multireddit public and accessible to other redditors, you can uncheck the "private multireddit" checkbox.
Once you've entered your name and made your decision on whether to make the multi private or public, tap "Add."
Now click "Add Subreddit" and enter the first subreddit you want to add - for this example "Guitar". Then I tap "Submit."
I click "Add Subreddit" again and add "luthier." Now when I hit back, I see a custom subreddit named ~guitarstuff. When I tap that, I see all my "guitar" and "luthier" goodness in one view.
reddit's official Multireddit replaces our previous Custom feature. If you have Custom subreddits from an older version, you should be prompted to convert them during upgrade.