Are pins 0 and 1 (Rx and Tx) parallel with the USB jack? Can I connect another USB jack th 0 and 1 and use it to upload sketches?
No. For many reasons. No. USB is not TTL. You need an adapter to connect rx/tx pins of arduino to USB. And the on-board adapter has the DTR line connected to reset the Atmega before writing a program into it. Without it, you would need to push the reset button in the right moment.