In the settings screen in Capex ( press II ), you need to change the window setting to either Software or Hardware Scaling ( note: Hardware Scaling is still actually software scaling). If you launch the game now the screen will be scaled to fit the Caanoo screen...However..
There is a bug in Capex where the Window setting is not being saved, so for the time being you will need to set the Window setting everytime you start a game (that requires scaling ). I'll fix this issue at some point but at the moment I'm considering just implementing a menu system inside of FBA as it will makes things easier...I've not decided yet.