You should not have a problem in either case, as you are currently married.
Even if you are the primary applicant, you would have documents that suggest your current partner is legally married to you and your stepchild is his legal ward, which makes him/her your legal stepchild.
If you are the non-primary applicant, even in that case it won't be an issue because you would be having documents suggesting that you are their legal partner.
In all cases, since your partner is separated from his/her earlier partner, your partner might need documents that suggest that your partner has full-time custody of your stepchild and your spouse's ex-partner should not have a problem with your stepchild gaining PR of a different country.
This is very generic advice and may not suit your jurisdiction as I am not aware of your location. I would advise you to seek consultation from a family and a Canadian immigration lawyer in your jurisdiction to get more clarification.