How to program a MSP430FR5959 using pogo pads?
Based on this schematic and assuming 4-wire JTAG, you should add 8 pads to your PCB and wire them to the MSP430 pin of the same name:


TDO
TDI
TMS
TCK
NRST
TEST
VCC
GND


You should then build an adapter cable for your JTAG debug probe and wire it to the JTAG pins of the same name except for VCC:


If you want to power the board via the JTAG debug probe during programming, wire it to pin 1 of the JTAG adapter (VCC_TOOL).
If you want to use the boards own power supply during programming, connect it to pin 2 (VCC_TARGET).


If the JTAG pins TDO, TDI, TCK and TMS are exclusively used for JTAG, you could connect them to VCC. Then you don't need the TEST pad and pin and can get away with 7 pads for the pogo pins. If you connect the TEST pin/pad, you can use the pins both for JTAG programming and as GPIOs.

This assumes that your board already contains the pull-up resitors and capacitor on the reset pin. If not, they need to be added as well.