I just got some and they have made a great improvement in my running, but do I need to put them in my bike shoes?
not usually, especially if they weren’t made specifically for cycling shoes. I make over 1,000/year and they are generally for Root biomechanics (i.e. heel-toe propulsion) and I “assume” yours were along these lines. Your foot has very different stresses inside a snug cycling shoe attached to a pedal.
Generally you need to have a special pair made for cycling shoes that will be much thinner. They can also work in ski boots, some dress shoes, etc; but a “standard” orthotic won’t fit in your cycling shoes.
Rroof,
Would they help if I have high arches and need more arch support? I am using Shimano TR-02 shoes and it appears the carbon sole has also contributed to pain along the bottom/out side of one foot.
What are your thoughts on the Specialized TriVents? THey seem to have a unique and perhas better design to support feet.
Barefoot
I wear custom orthotics in my bike shoes and not in my running shoes. I can find shoes to fit very well while running but I have not been able to find a good fit in a bike shoe so I use my orthotics in them.
I wear the same pair of orthotics in my running shoes and cycling shoes.
I had some arch pain when I didnt and the pain went away when I used them…so I must be doing something right 
I use to wear orthotics only in my running and walking shoes and not in my bike shoes. It would feel like some one put a golf ball in my running shoes during a race or brick workout. Once I started wearing orthotics in my bike shoes the problem stopped.
I’m also under the impression that you’d need another set for your cycling shoes. I just got a pair (SoleSupports) for my running shoes, through my PT. He mentioned that they’re apparently making (already made?) them for several Postal (now Discovery) team members. I have yet to try to fit them in my cycling shoes, but I suspect they’ll be too long. Good luck.
Yup - you can’t argue with “success”. Actually, I really have no way to “measure” forces on the foot if there seems to be a problem in cycling shoes. Obvious biomechanical issues are easy on exam/X-ray, but I rarely find any of these in Triathletes (or they probably wouldn’t be in the sport anyway). If it works for you, do it! (no matter what your PT, chiro, physician says).
I’m speaking in general terms of medical advice over the internet.
Barefoot - I also use the Shimano TR-01 (same a 02) and I have a lot of people with lateral (outside foot pain). I’m not sure why. I also have this, but only on long (>50 miles) and I’ve yet to figure it out. I have neutral to flat feet and I’ve adjusted my cleats. I’ve had some relief switching to speedplay Zeros from Simano SPDs. I really like the shoes, but I think it might be them. I do like the Specialized shoes and use them for training and on my road bike.