Anywhere there is a surface area of water that is exposed to air, especially areas with greater surface agitation, you will offgas. The CO2 will indeed go into the main tank where some of it will be used, and some will be offgassed. Anything not used right away will continue through the tank and to the sump, where more of it may offgas.
I'm not saying that you will lose a ton of CO2, but you will lose more than you would without the sump. It may just be a trial and error process, because I haven't heard of anyone else running a large, CO2 injected, planted tank with a sump.