Orthotics

I used to wear Orthotics before but discarded them. I have been running fairly seriously for a couple of years now and from Sept last year until February of this did 4 half marathons. No problem while running but knees ache after running and sitting and rising from a chair became uncomfortable. I visited a Podiatrist who said I definately needed orthotics as I over pronate and am basically out of alignment. Walking at 10 to 2 etc..Of course being 50+ altering this is a bit late in the day. However I have the orthotics and wear then for work and for gym work and do feel the difference I am also doing a varied stretching routine which is helping to ease this knee problem. Again diagnosed as an alignment problem and not Runners Knee.
Okay finally my question is as I have stability shoes for running do I need to fit the orthotics in them also. I used to run in New Balance but became very disapointed with there durability having to run on roads as there is no other option. I now have Brooks GTS which I am well pleased with.