So will they have the same abilities and stats as the enemy they are skinned as? Or will the Borg be using phasers and photons?
Phasers and photons. They'll just have a new skin but will still behave like their root encounter, whatever it is. If you really want it to happen you can try thinking up some kind of explanation for their unusual behavior.
It depends what you want to do, but if you want these "friends" to fight other enemy groups to give the appearance of a larger battle, you can use invisible walls to separate them from the player.
Say you want the player "allied" with the Borg, and together you want to fight the Undine. Well set up some Borg encounters and some undine encounters to fight each other. Then put in encounters for the player to fight. Between those, put in a nice big invisible wall or two or three. Then it looks like the player is fighting Undine alongside the Borg.
You can go further and tie in the Borg encounter to your mission objective to drop the invisible wall when they are destroyed. So lets say you have to fight an Undine fleet. You set it up so the Borg are outnumbered and should lose the fight every time. You can make the defeat of the Borg group deactivate the invisible wall so the player can come in and clean up the rest of the Undine. Of course if the Borg win, that could cause problems in the mission.