ATmega2560 bootloader to use more i/o pins

oh..
and if i loaded the Bootloader then how do I load the Sketch via serial port
Should I use 232 or USB ?

Just to let you know I didnt put on my board USB (only ISP)
So is there a way to use an arduino UNO as the USB port and connect it to the At2560
Or should I use the RX TX port (with what SW should I do that)

Thats it for today
Sorry