Hilly.
You probably remember I had to put out of FLM last year due to injury, this was due to knee pain, but due to the fact that I do over pronate and my lefy leg is 3/4 inch shorter than my right and with a combination of mileage over the years this was the main reason for the pain in knee.
I had orthotics fitted last April, and it has been a slow progress but I am back running fairly well now and no problems.
My left orthotic is built up much more on the heel to raise me up, the orthotics seem to fit better in some brands better than others, but have no problems in putting them in my racing shoes.
I can't really answer personally about an orthotic in one shoe, but if you are having one specifically made then the one orthotic should work, I have dealt with quite afew people using just one orthotic.