When working up a load with magnum primers I don't do anything different nor do I make any reductions in starting or ending loads. I just load normally, work up the load and look for pressure signs.
This is especially true of 30-06 loads, which for the most part the loading manuals grossly under load because of numerous weak actions once made in that caliber. If you have a strong modern bolt action rifle of recent vintage you can work up 30-06 loads to well over book max. Most book loads for the 30-06 are capped at 58k PSI (60K SAAMI MAX PSI), but the 30-06 case is constructed identically to the 270 Win case, that has a SAAMI max PSI of 65K.
At one time years ago I used nothing but CCI 250 primers, as I had more rifles in magnum calibers than standard ones, and never noticed any remarkable differences in my loads. Even today, I stock only CCI 450's for those cases that take SR primers. Though that is more a function of primer thickness, as I make more loads for an AR15 than I do for SR bolt guns.
But I am curious as to what bullet your contemplating loading in your 30-06, as Hodgdon Reloading does not use the powder for bullets over 180 grains, and the smallest starting load they list for it is 45 grains of IMR4320.....