How to wire a mega328p-AU

Ive added the capacitor to V3 on the CH340C and swapped RX and TX, in the schematic they've added LEDs so I've decided to put them back in how they've done in the schematic.

Do I only connect the inputs (A pins) to ground and none of the Output (Y pins)?

As for the LED I don't think I need a PWM signal, as by holding the pin HIGH it will turn on the Red, green or blue diode in the LED, and I'm only using it a state indicator (Stages of the flight of the rocket) so I'll only be using one colour at any point.

I'm pulling off a pre-bootloaded Processor from an Arduino NANO clone, but if I was to boatload the chip I should be able to by returning the CPU with an Arduino UNO and program code from the micro-usb via the Arduino IDE (at least in theory)

This is the schematic I was basing it off of, how would I have to change the header pin to be able to so do?

thank you again for helping so much - Harvey