you will use the jumper in place of the 100K resistor on the switch ONLY if you mount the 100K directly to the tube socket. If you are using the relay board, you will not use a jumper. Instead, follow the builders guide for the 5V Relay board:
http://www.trinityamps.com/docs/TRIWATT_OD_Relay_Manual_5V.pdfSince you mention you not sure what is going on, I'll try to describe the overdrive circuit.
Each half of V1 serves as the preamp for the bright and normal channels. The signals come off the plates of V1 (pin 1 and pin 6) to the respective volume controls, and then to the two 470K mixing resistors (R9 and R10). From there, the junction of these two resistors serves as the input to the next stage. The OD switch is basically routing this input through V2b (pin 7) and then to V2a (pin 2), which then goes to the tone stack ---OR--- bypassing V2b and going straight to pin 2. Thus, V2b (pin 6,7,8) serves as the OD circuit, as the signal from this circuit is cascaded into V2a (pin 2) when the switch is engaged (pulled).
As I mentioned, the second triode of V2 serves as the cascaded OD circuit....the signal input is pin 7 (grid), and the output is the plate (pin 6). From pin 6, the signal goes through a coupling cap (C4), then on the the 1M pot (OD control; VR3), and then to the 100K resistor (R47). The switch, when pulled, connects the other end of the resistor to the shielded wire leading to first triode of V2 at pin 2, the grid. The end result is cascading the mixed signal from V1 into V2b, then to V2a, then to the tone stack.
When the switch is in the off position, the "other end" of the 100K resistor (R47) is not connected to anything, so anything that happens in V2b has nowhere to go. At the same time, with the switch in the off position (pushed in), the mixed signal coming from V1 (where the two 470K resistors are; R9 and R10; orange "straight line" wire) is sent directly to V2 pin 2. This results in a bypassing of V2b. You can see that when the switch is pulled (OD is on), the signal coming to the switch from the mixing resistors along the orange wire has no place to go, and instead takes the closed path from the mixing point straight to pin 7 via the shielded wire, where it travels as described in the preceding paragraph.
The 100K resistor (R47) is only connected to V2, pin 2, when the overdrive switch is engaged. R47 is not at any point connected to V2, pin 7.
I know I suggested earlier to perhaps build the amp without the relay board in order to simplify troubleshooting, but on second thought you may want to proceed with installing the board right off the bat. That way you don't have to rewire anything. Doing it this way will result in the 100K resistor being moved to the relay board, and you will wire everything as described in the 5V relay board builders guide.
The Triwatt is a great amp but probably the most complicated build I've done. Take your time and quadruple check everything. As with any amp, good lead dress and wire routing are critical. But the cascaded OD circuit can be a source of gremlins. Use the shielded wire as recommended and minimize wire length whenever possible.
Good luck!