It is a work in progress, so Atom is adding and adapting features based on user feedback. So you will find some feature may work, but by the same token Atom may change or remove them as he sees fit.
At present you will need to write a method in Lua to transmit .syx files to your device. The program manager is Atom’s attempt to simplify that task and negate the need for a Lua method, however the function of no two MIDI devices is the same. This is a big undertaking and may take some time for Atom to resolve.
Lets us know how you get on with the Lua method.