Hi Andria,
I have not used woopra in a while because my traffic is much higher than their free service limits allow, so it is possible they have changed things but as far as I know you just need to check the box in Administration > Site Settings > API Keys > Enable Woopra Tracking script. And you need to have your sites registered with your woopra account via the woopra web site. It knows what host name the traffic is coming from so there is no need to enter any account info in mojoportal.
Hope it helps,
Joe