I wear custom-made orthotics, but haven't noticed any problem. Mine are full size, however, so they fill the footbed entirely.
The neoprene insole is a good idea, some people remove the original insoles from their shoes, some keep them in. I don't know whether that would that be possible for you? If not, then carry on with the insoles as you are doing, but make sure that they are not too thick to offset the benefits of the orthotic.
I do find that they lift my feet slightly higher in the shoe, so fit around the ankle area is sometimes an issue, but as I've only found one pair of shoes that both accomodates the orthotic and suits my gait, I stick to the same. If it's a real problem, I'd go back to the person who made your orthotics and ask for advice.
If you are getting new shoes, talk to your shop when you buy your shoes and see what they could suggest - thicker socks perhaps?