"Tough As Nails": Foot pain and Orthotic?

I recently experienced an extremely sore big toe.  I went to a pediatrist who after an ex-ray determined that I have two bones in my big toe that are enflmamed between them.  He described the pain as being an overuse injury and because of my high arches gave me an orhotic to use.  He told me to wear them all the time and to run in them.  It has been two weeks, my toe still hurts and I'm still adjusting to the orthotic.  Has anyone ever worn or used these?  I have never even heard of them untill now, so I'm just wondering if this is common, if it is permanent and with only two weeks untill the marathon, I need to decide if I'm going to run at all, or if I do run, will I run using the orthotic.

Also, I experience arch pain the first steps out of bed in the morning.  Is that one common?