What If I removed the Atmega328 from the UNO board then connected the TX , RX pins from the Atmega328 to the UNO board , will that work ?
This is what I've been doing and it works great. The only down side is you'll be removing and replacing the '328 a lot on the uno as you switch between programming and debugging. If you're going to be doing this frequently, it may be worth looking into getting a standalone programmer.
That will work but there is an easier way. On the UNO board just jumper the shield reset pin to a shield ground pin, that will force all the UNO's 328P I/O pins input to high impedance input mode so will have no effect on anything wired to pins 0 and 1 to utilize the USB serial function.