It's defaintly more of a manual process.
First you have to unzip the epub and then use Book Designer 5 to join the multiple html files together into one big html file then import it into the program.
It doesn't take long to edit the file, you just need to mark the Chapters as Titles so it knows to make a TOC from them. Book Designer and Fiction Book Designer will auto detect most of the titles when importing then you just go through the Title list in the Element box and correct any that aren't Chapters or Headers.
Once that is done you can click Create the FB2 button, enter the info in the boxes and click the Make button and it's will create the FB2 book.
You do have to open the FB2 in a text editor (I use PSPad) and do a search and replace for amp; to &
I use the same method for my epubs as well except I save the file as htm then import into Calibre. I also add inline TOCs (Using the TOC option in BD5) to my epubs which work most of the time in CR3. I then use this regex
//*[@class = 'title']
in Calibre's Detect Chapter and Insert Page breaks boxes to make a nicely formatted epub.
The programs aren't perfect have quirks but I'd be lost without Book Designer and now FictionBook Designer. You don't need both though you can use either or but I use both for various reasons.
When I discovered CR3 I spent 3 weeks converting my mobi files to epub and now I convert to FB2 mostly. I also zip the file and add .fb2 to zip and it works great and is smaller then a epub file. (Thanks Dave for all FB2 info!)