I may be wrong here, Because im also pretty new setting up carbon filters and im actually doing mine right now, but from what ive read and learned so far you should be okay. As long as theyre both 6 inches you can connect them with a hose clamp or with flexiduct and tape. It should still pull the air even though you aren't maxing capacity you might just have to let it run longer to scrub the air because the fan is less powerful. Also if you google carbon filter setup it should pop up a 2 minute video on youtube about how to set up someones kit you can buy but it gives a good visual on how to set one up even if you dont buy their kit.
Hope this helps - DD