I have a lot of history with ortotic insoles. I've seen about half a dozen podiatrists over several years and each has come up with a different prescription. Each had different techniques (or lack thereof) for coming up with whatever prescription. The first lot were all awful and injured me. The last more comprehensive ones which address three, not just one, problem my extremely hypermobile feet have, immediately felt so much better for my whole body (and building up gentley went out of the window! as my body rejected the old rubbish ones).
The advice certainly is that you should build up gentley as you are changing your biomechanics. It could be that any aches and pains to start with are just adjustments to the new biomechanics. However, it could also be that the orthotics are completely wrong for you. You need a proper check in person by someone competent and who knows all your problems to ascertain which. There are 26 bones in each foot and they are complex bits of engineering. Something off the shelf may or may not be suitable for you. You need to be checked with the orthotics to see.
My right leg was APPARANTLY shorter than my left, but it was a functional short leg due to the right foot overpronating a lot more than the left. Ie not a true short leg and a heel lift did not help or may my two legs equal at all. I think it just made my pelvis more twisted. Some podiatrists just don't know about this surprisingly. I despaired.
If you haven't automatically got a follow-up appointment with the podiatrist a few weeks after starting to wear them, you should go back and have one anyway. To do a good job, they need to see how your complex bits of engineering at the end of your legs are working in practice with the orthotics. When I finally after many years got the good orthotics, the right one was tweaked a little after 3 weeks on the outside edge.
By the way, I am the joint local group leader for South Central if you would like to join our little get-togethers. We sometimes meet in Oxford and sometimes in Handy Cross, just for a pub lunch or so. Let me know if you are interested.
Joint group leader for South Central (Bucks, Oxon, Herts)