As of today the freesat ios app is available to download from app store, providing a guide and the means to remotely set timers on freesat freetime units.
Link to news item on freesat website
Link to post on freesat community forum
https://itunes.apple.com/gb/app/freesat/id748306909?mt=8
You can also register and pair your box(es) via freesat website.
(the above is also applicable to the HB1000S)
I've been told It is important that you do not have any failed timers listed, so delete them if you have any, before trying to set any timers via app.