you might be charged for 2 fees if you both qualified... i read here some encountered double charging of credit card bec they sent two applications (1st set was incomplete) with one principal applicant's name both sets... so in your case theres a higher chance of charging you twice for 2 applications with different principal applicant.
I suggest which I also plan to do once our 1st application will be rejected is to have another set of application with diff principal applicant since we are both eligible under 38 NOC...
theres some waiting time 45-60 days for your AOR which means you are eligible but you are safe with one fee... slowly but surely ;D
thats just my advice & its up to you to decide.
goodluck!