You can use the "In SC" button to make your Eq settings apply to the internal sidechain.  However, bx_console N's external "Key input" functionality is totally separate from this, and is a bit more limited.  You can use the "Key" button to enable an external sidechain input, which will be applied to the Gate.  The external sidechain can't be applied to the Limiter/Compressor -- only to the Gate.
So to sum up: Use the "In SC" button to apply your internal Eq settings to the L/C, and use the "Key" button to apply an external signal to the Gate.