I have been told that to use an apprentice to assist in lab work, they must be the same house as you or they do not understand your specific take on magic theory enough to be of assistance.
is this true? and if so how do bonisagious handle it when they take an apprentice from someone of another house?
No, that sounds more like someones house rule addition.
And since Magic Theory is meant to be the big thing that brings the order together, i think its a bad idea to separate the houses this much.
then what about such skills as faerie magic? does that this mean you could have a bonisagious with the special house skills and abilities?
Yes. It's easy to learn Faerie Magic, and Enigmatic Wisdom, for that matter. Both houses are very free with their "secrets", because to learn them is to think like a member of the house, so it is more correct to think of them as a member of the House of Faerie pretending to be a member of house Bonisagious. It gets a lot trickier with an apprentice from one of the "jealous" houses, like Verditius. Given that the last thing learned, as a rule, by the apprentice is the house mystery, you would have to find a mage which taught his apprentice early, then use your house rights to take the apprentice, and then survive the Wizards War and the tragic accident your new apprentice is going to have....
Anyone with Magic Theory and The Gift can assist in the lab. If you are trying to use a special ability of the helper's House, I would agree that you need to be in the same House to pull that off. For example, a Bonisagus could help a Verdidtius in the lab, and the Verditius could use all his special abilities, though I doubt that he would. If the Verditius helps the Bonisagus in the lab, the Bonisagus does not get any benefit from all those cool bonuses the Verditius has when he is alone or in charge.