I've read several books each alleging varying degrees of her involvement from complete ignorance to full on director of the scheme. How can we be sure?
It will be great to know which books you have read.
The Bartholomew's Day Massacre comprises of several distinct stages, namely the assassination attempt on Coligny the leader of the Huguenots, then the order to murder the Huguenot leaders in Paris, then the communal murder frenzy, and finally the spread of violence to the provinces.
While traditionally there is tendency to blame Catherine de Medici for all three, more recent critical examinations analyze her within the context of the four stages.
Did she order the assassination attempt on Coligny? Traditionally, de Medici was blamed as the mastermind, with the support of the Guises. The thinking goes that if it had succeeded, it will have significantly weakened the position of the Huguenots both in France (removing the influence of the Huguenots on Charles IX) and elsewhere (Coligny was said to have designs on French involvement in religious wars in nearby Low Countries). The fact is that the shot was fired from a building owned by the Guise family, who had openly opposed the Huguenots, so it can be argued it made more sense that the Guise faction, or somebody from their faction, would be the one to arrange it.
Was there a pre-existing plan to murder Huguenot leaders in Paris? It's quite easy to argue that it there was indeed such a plot, then why attempt to kill Coligny ahead of the plan? The argument is then reduced to, who instigated this murder, was it de Medici or was it her son Charles IX? Up to this point Charles IX had ruled under the shadow of his mother Catherine de Medici, so the distinction becomes very, very murky. Most agree that this is an over-reaction due to fears and tensions in Paris and that whichever way this was proposed, de Medici endorsed it. If this was an over-reaction, keep in mind the 4000 Huguenot military contingent stationed outside the city, led by Coligny's brother.
Communal violence in Paris. There is less argument here that the pro-Catholic city militia mobilized to secure the streets while the Royal Guards carried out murder of the Huguenot leaders ended up fomenting fear and violence by the Catholics against the Huguenots. Most historians say that the Catholic citizenry was led to believe that the 4000 Huguenot military contingent stationed outside the city was about to strike, when they saw the city militia deploy on the streets. At the same time, there was already much resentment and hatred. Coligny's dead body was mutilated and put on mock trial, as were those of other leaders.
What about the provinces? The timing of outbreak of violence tells us a lot. Most did not start until mid-September, weeks after the Paris massacre, some even later. So it was spread of news that fomented them. Further, by this point Charles IX had issued orders that local governments keep the peace, and evidence points to populist uprisings leading to violence. Exceptions, of course, are towns where Protestants were in the majority, such as La Rochelle.
All of the above are mostly based off of Mack P. Holt's French Wars of Religion.