Hi @bhindhiya
Personally, I'd recommend following @Juraj 's suggestion regarding adding a custom board.
It's possible to create a new board entry in the Arduino IDE, but this is quite involved. I've described it in the following Arduino forum link, but it was written awhile ago back in 2016 and some of the details might be out of date: https://forum.arduino.cc/t/adding-custom-zero-based-boards-to-the-arduino-ide/394499.
The bottom line is that the closer your custom board is to the Arduino design, the easier the integration. If you use a SAMD21J18A together with an external 32.768kHz crystal and the same memory footprint (as the SAMD21G18A), it will require minimal changes.
If you use a SAMD21 with a different memory size, (SAMD21x15, 16 or 17), this will require modification to the bootloader and Arduino's SAMD21 core code. If you use one of the newer non-default SAMD21 variants then it will additionally require a compatible version of "bossac.exe", the program used to upload your sketches over the SAMD21's native USB port.