You can not break in your boots. Instead, the boots break in your feet.
They will not change in size or shape. The sturdy soles will never change either, they can only wear out on the bottom. Eventually, after a million steps, some of the leather or construction will break down and disintegrate, but meanwhile it won't stretch to conform to your foot.
What happens is, your foot conforms to the boot. That's not really bad, because your feet are flexible and alive. But sometimes the joints of your arches, or toes, or heel will thicken or thin as a result of the constant pressure-changes and movement of the boot. Possibly some joints will expand to form a bunion or other bump.
If your toes are hurting on the descent, you're also likely to over-stress your big toe-nail with each down-step. You can bruise the nail pretty bad because it's a repetitive-stress injury. Very repetitive.
In my own experience is different for each pair of hiking boots I've owned. I always buy sturdy hiking boots or backpacker's boots. Not cheap ones: brands with good reputation in my own community. Usually all leather, usually Vibram.
Boots #1: totally wore out the Vibram tread, then the toe leather cracked.
Boots #2: the toe outer (top) flexed against the boot-lace, so the internal support wore out, and chafed my toes.
Boots #3: although these boots felt good, in fact the body was too soft. On scree they'd often roll with the rubble and I'd stumble.
I lost a lot of blood before I realized how they weren't working for me.
Boots #4: light-weight hikers, a little too roomy in the toes, so the down-hill pressure pressed against my toenails with every down-step.
I lost one big toe nail. Also, if I tie the laces tight, the down-pressure on my arches prevent the foot joints from flexing.
But otherwise they're so comfortable I continue to use them, but only below the tree-line.
Boots #5: Again, leather upper, Vibram sole. Still hiking. These things really work on rough terrain.
Really expensive, but so light-weight that I love them above tree-line, on ridges and summits.
If your boots fit, and if they work for you, then you should accept that they are what they are, and you can't change them.
But the tricks I use is socks.
The first trick is "wool socks". This compensates for a lot of conformity and movement. Try different brands. If you hike on snow, the bonus is they keep you warm.
The second trick is "liners". These thin, light-weight socks are meant to be worn as inners. They help you by isolating the foot flex from the boot movement. They don't always help, and you can't always find them. But if you can get a pair, try it. They might help you, or they might not.