ASA. I asked this question to a recruiter. As far as I could tell, there is no Standard Procedure for this, you will have to speak with the people in charge of your BMQ and work something out.
There are Muslim Chaplains in the Canadian Army who can help with this. Search for them and talk to them (as your recruiter to put you in touch). The Muslim Chaplain's can then communicate with the NCOs in charge with regards to this on your behalf.
Here's the gist: For the Canadian Army, religion is a personal choice, and therefore, it is not guaranteed that you will have time to pray every time. However, most of the time they will try to accommodation. My suggestion is, you contact the Muslim Chaplain, and at the same time, you print out a prayer schedule and speak with the NCOs in charge at your training. The way I approach it with them is, praying just the obligatory prayers takes about as much time as a bathroom break.
Good luck and let me know how this goes for you.