Programming ATmega328p on external board with FT232R I am making a 100W AC-DC linear power supply, for which I want to show output Voltage and Output current on LCD display. I already used shunt resistor and voltage resistor to bring both values to analog pins on my ATmega328P in DIP socket, which has an Arduino bootloader on it. I want to programm my ATmega328P on the board without taking it off everytime and putting it into Arduino UNO board to just programm it and put it back, so how can I integrate a programmer onto board? 
I intend to use the FT232R ic, which I think would work more than fine for this application.
On finished product I want to have a USB connector on the case just to update/correct the software.
I suggest use ICSP(In circuit serial programming) feature of the Atmega 328 chip. Grab the .hex file from the arduino IDE and a USB ISP external programmer to write the program to the chip. Here you will have to use a 6 pin header on your custom board to take out the pins which are used to program the atmega.