I just solved it. First write the notes without cross-staff, apply the fermatas, choose “one per side of staff”, highlight one, flip it over and finally select the low E in the right hand and press M. Too complicated… 
There should be something in Engraving Options that makes handling fermatas easier.
Yes, I think the key here is that cross-staffing often needs to be the last step, so you can be very clear about what is on which staff.
Maybe this option?
And then change the color of the breath mark into white.
- Write mode
- Select notehead
- Select breath mark
- Engrave Mode
- Properties
- Color
- White
