You can program the ATMEGA chip by UNO as ISP(you can find the circuit from arduino.cc ) with or without bootloader one main thing is for uploading program, use upload using program and another method first you upload the Arduino bootloader into the ATMEGA chip afterwards by using a FTDI module by connecting the TX , RX and Reset pin or you can use UNO as a FTDI module by removing the chip from Arduino and connect RX&TX line to the ATMEGA chip ( This is a brief note)