The thing about a schematic is that it is an abstraction of the actual design - it really doesn’t need to look like the actual component, it simply has to facilitate a logical view of the circuit. So, for example, here is an Amega 328P-AU from the KiCad library. The symbol looks like this:
but the actual chip has a completely different physical layout. It doesn’t matter and, in practice, you often edit your symbols to fit your schematic layout more neatly - for instance you might swap the PORT C and PORT D blocks around, split them up or invert the order so that it fits your design layout better - it will still connect just fine as the pin numbers define the physical connections.
You can stick your connector symbol anywhere convenient and just connect to the pins you want to use. You don’t even need to run a wire between the the pins you wish to connect, you can simply attach a label on both of the connections you wish to make which declutters the layout further.
You may benefit from using a template for this board - a quick search turned up this which includes a link to, but like all things, you probably need to verify that it meets your needs.
and the repo