You can connect your own board to the same ez430 stick as you used before for programming the same MSP. Provided you make the proper connections. Keep the wires and traces very short. And the supply voltages must match.
As for the bootloader: almost all MSPs have a factory-programmed bootloader. On 5x family, it is in flash and can be replaced, on all others it is in ROM. But even the flash version is protected against accidental deletion. However, the bootloader does not use JTAG and the JTAG programming pins. It uses a serial connection through a software UART on the timer pins (not using the hardware UART, if any). An exception are the parts with USB controller, which use USB. The bootloader doesn’t support debugging. It’s just for uploading a new firmware.
Anyway, I recommend buying and using a FET430UIF for own PCBs. It doesn’t provide an application UART (you’ll need separate UART connection anyway if you don’t want to deliver an EZ430 with your product), but it supports an adjustable supply voltage as well as running with targets that have their own supply. And supports all MSPs out there.