The spare donut should always be used on a front wheel. So if you have a flat on a rear tire you will need to move a front wheel back and put the spare on the front. Definitely go slow and limit the number of miles you ride with the spare on.

Auto-racer just had an experience with a flat and he posted this info:

"I did learn a few tricks when it comes to driving with the spare and TOD. Left foot brake when you come up to a light with light throttle. Otherwise the TOD makes a nasty noise as it downshifts. Also drive slow as the instructions say... Otherwise the Tod senses road speed differences and starts to engage/disengage 100% and makes a very nasty grinding noise. I found I could stop this with left foot braking again... Just step on brake while still on gas to disengage TOD".

I dont think it is only the TOD that is affected - was there something concerning the differential that causes a bigger problem (?)