Here's a few things to try:
It's often claimed that good trainers no longer need wearing in. This is simply a generalisation. Even a pair of good shoes with a good fit may cause blisters and discomfort for a couple of weeks, especially if the last/brand is different from your previous pair. Feet and gait adapt to the shoe, and it takes alittle time. Callouses on the foot are a part of this 'adaptation'.
I run up to 140km per week, and at that volume persistent discomfort from blisters can have a noticeable affect on gait/stride and quickly lead to injury in other areas.
I had similar problems when I first started out with my current 'best' pair of marathon shoes - deep blisters around the heel AND under the ball of the forefoot. I did a bunch of things to get me through the difficult first two weeks. NOTE: If the problems persist after a couple of hundred km of training then chances are the shoes just aren't right for you.
Here's my recommendations in no particular order:
1) Buy a pair or two of twin-layer socks. They're designed specifically to alleviate/prevent blisters. In my experience they work brilliantly. E.g. Ron Hill 'twin skins' - expensive but worth every penny
2) Use a shoe/foot powder after running, I find it helps with blisters but don't know exactly why. One possibility is that it sucks the excess moisture out of dead/near-dead skin. I don't know.
3) Use a pumice stone to smooth out any rough edges on old callouses/blisters.
4) Occasional moisturising of dry areas of dead skin - helps keep the skin live and elastic, prevents tearing.
5) This worked brilliantly for me - I padded out the area either side of my blister/friction-point with a little rolled-up toilet roll. It relieved the pressure and friction at the blister and allowed me to continue running while my shoes softened up.
6) Experiment a little with the lacing of your shoes. Relieve the tension around the upperfoot and add tension to the lower foot and vice-versa. Try different lacing patterns - there's a great article on the US version of this site (.com) and maybe it's here too...
7)Plasters are obviously a temporary fix and frequently come off. A more radical solution is to use the very strong,sticky and effective surgical tape that is normally used for holding down bandages/padding. The glue on this stuff is very strong, and it isn't quite meant for the following purpose: I sometimes apply this directly to the skin if I have a sore-spot/imminent blister/freshly burst blister but want to guarantee zero discomfort during a race. This is something you should avoid doing regularly - post race you'll probably rip most of the dead skin off your foot when you remove it. Potentially painful, and liable to temporarily exacerbate the problem post-race.