There are actually rules for this in the official supplements. Look at p. 259 of the Core Rulebook for the rules of common cloaking devices. A phasing cloak device should, of course, provide the phase cloaked trait to the ship using it, working just like the cloaked trait, but allowing to pass any ‘normal’ matter (there might be other things out of phase the ship could normally fly through but cannot while cloaked. Use this as a plot device.).
For the phase cloaking device itself, look at p. 62 of the Operations Division supplement. Additional to a description, it lists the opportunity and escalation costs of this type of equipment (see p. 184 of the Core Rulebook).
In addition: Since the technology is so new, I would assign a prototype trait (p. 186 f. of the Core Rulebook) to a phase cloaking device. I would think of raising the difficulty to cloak by 1. I would also assign the task to cloak to the engineering station instead of the tactical station. I would also think of modifying the decloak action to a task (difficulty 2).
Since the technology is so dangerous, I would raise the escalation cost by one or two. I, personally, would also use most or all of the Threat generated by the escalation cost to raise the complication range while the phase cloaked trait is active.
Last, but not least, since the technology is in violation of the treaty of Algeron, I would consider each use of the technology as a negative influence on reputation rolls after the mission.
In case there’s a mission directive to specifically uphold interstellar law and/or treaties affecting Starfleet, this directive would have to be challenged at least by the characters ordering to activate and activating the device. I would say that this does not fall under the standard prime directive that is always in effect to be not too harsh. But you might as well consider every breach of the Treaty of Algeron ipso facto a breach of the prime directive, meaning that the prime directive would have to be challenged any time the device would be used.