The powder you use is more the reason for choosing a mag primer than the case you're using.
Over the chronograph, I've found that in the smaller (standard as opposed to Magnum) cartridges there is little difference between the two primers, YMMV.
If you do much shooting in the cold, you MAY want to choose the Mags, anyway.
The usual advise to start lower and work up, is good.
The hottest Mag primers out there are Federal 215s, so I would drop back .5-1.0gr from the recomended load...not the max!
IMO, AA2520 and BLC2 have no need whatsover for a Mag primer in the '06, tho' WW760 may use them.
I would think of trying one of the 4831s, or maybe 7828. I don't know what powders you have, or can get locally. I also don't know what bullet you intend to use, either.
The '06 can be interesting to play with.
Have fun,
Gene