On running the model twice

It sounds like you've got a good grasp of it. I'll go into a bit of details for anyone else with similar questions.

With GHGenius 5.0 and later some effort has been put into minimizing the components of a fuel cycle that have emissions from both the feedstock and finished fuel portions of the lifecycle. In practice, what this means is that the fuel production is just the upgrading of the canola oil and does not include any emissions associated with producing the oil.

Looking at the HRD pathway we can go through and identify what each part of the pathway is on Upstream Results HHV.

Fuel Dispensing: This is the emissions between the fuel arriving at a service station and being put into a car's tank. Associated with the finished fuel.
Fuel Distribution and Storage: This is the emissions from the upgrader, refinery, or whatever the producer of the finished fuel may be, to the service station. Usually includes both transportation and some storage emissions. Associated with the finished fuel.
Fuel Production: This is the emissions from producing a finished fuel out of a feedstock. In your case the canola oil to HRD, other examples might be corn to ethanol, or electricity and water to hydrogen. Associated with the finished fuel.
Feedstock Transmission: This is the emissions from transporting the feedstock to the facility that produces the finished fuel. Such as your canola oil to refinery or from corn farm storage to an ethanol plant. Associated with the finished fuel, and generally proportional to inputs the user sets on the Input sheet.
Feedstock Recovery: This is the emissions associated with growing or producing a feedstock. For fuels such as your HRD and biodiesels it is emissions such as farming or collecting the raw feedstock prior to crushing or oil production. Associated with the feedstock.
Feedstock Upgrading: This is the emissions associated with producing, crushing in your case, the feedstock. In the case of oils this is related to the crushing energy defined on the Input sheet. Associated with the feedstock.
Land-use Changes, Cultivation: This is emissions associated with fertilizer use and and land use changes from growing the crop. It does not include energy inputs for farming such as tractors, those are in feedstock recovery. Associated with the feedstock.
Gas Leaks and Flares: Not used in renewable fuels.
CO2, H2S Removed from NG: Not used in renewable fuels.
Emissions Displaced: This is the one spot where emissions associated with both the feedstock and the finished fuel are combined. In the case of canola HRD this is a combination of the gases and liquids coming out of the refiner, Coprods!AU118 in GHGenius 5.0f, and a second term that is related to the meal produced from crushing canola seeds. As you've identified, you need to take the second term with INDEX when running in your feedstock region and the first term from Coprods when running for the finished fuel.

But again, it seems like you've figured all that out and are on the right track.